Compositions for modulating gene expression

ABSTRACT

Aspects of the invention provide methods for selecting a candidate oligonucleotide for activating expression of a target gene. Further aspects of the invention provide methods of selecting a set of oligonucleotides that is enriched in oligonucleotides that activate expression of a target gene. Further aspects provide single stranded oligonucleotides that modulate gene expression and compositions and kits comprising the same. Methods for modulating gene expression using the single stranded oligonucleotides are also provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit under 35 U.S.C. §119(e) of U.S. Provisional Application No. 61/648,016, entitled, “COMPOSITIONS AND METHODS FOR MODULATING GENE EXPRESSION”, filed on May 16, 2012, of U.S. Provisional Application No. 61/648,021, entitled, “COMPOSITIONS AND METHODS FOR MODULATING GENE EXPRESSION”, filed on May 16, 2012, of U.S. Provisional Application No. 61/786,232, entitled, “COMPOSITIONS AND METHODS FOR MODULATING GENE EXPRESSION”, filed on Mar. 14, 2013, of U.S. Provisional Application No. 61/647,858, entitled, “COMPOSITIONS AND METHODS FOR MODULATING SMN GENE FAMILY EXPRESSION”, filed on May 16, 2012, of U.S. Provisional Application No. 61/719,394, entitled, “COMPOSITIONS AND METHODS FOR MODULATING SMN GENE FAMILY EXPRESSION”, filed on Oct. 27, 2012, of U.S. Provisional Application No. 61/785,529, entitled, “COMPOSITIONS AND METHODS FOR MODULATING SMN GENE FAMILY EXPRESSION”, filed on Mar. 14, 2013, of U.S. Provisional Application No. 61/647,886, entitled, “COMPOSITIONS AND METHODS FOR MODULATING UTRN EXPRESSION”, filed on May 16, 2012, of U.S. Provisional Application No. 61/647,901, entitled, “COMPOSITIONS AND METHODS FOR MODULATING HEMOGLOBIN GENE FAMILY EXPRESSION”, filed on May 16, 2012, of U.S. Provisional Application No. 61/785,956, entitled, “COMPOSITIONS AND METHODS FOR MODULATING HEMOGLOBIN GENE FAMILY EXPRESSION”, filed on Mar. 14, 2013, of U.S. Provisional Application No. 61/647,925, entitled, “COMPOSITIONS AND METHODS FOR MODULATING ATP2A2 EXPRESSION”, filed on May 16, 2012, of U.S. Provisional Application No. 61/785,832, entitled, “COMPOSITIONS AND METHODS FOR MODULATING ATP2A2 EXPRESSION”, filed on Mar. 14, 2013, of U.S. Provisional Application No. 61/647,949, entitled, “COMPOSITIONS AND METHODS FOR MODULATING APOA1 AND ABCA1 EXPRESSION”, filed on May 16, 2012, of U.S. Provisional Application No. 61/785,778, entitled, “COMPOSITIONS AND METHODS FOR MODULATING APOA1 AND ABCA1 EXPRESSION”, filed on Mar. 14, 2013, of U.S. Provisional Application No. 61/648,041, entitled, “COMPOSITIONS AND METHODS FOR MODULATING PTEN EXPRESSION”, filed on May 16, 2012, of U.S. Provisional Application No. 61/785,885, entitled, “COMPOSITIONS AND METHODS FOR MODULATING PTEN EXPRESSION”, filed on Mar. 14, 2013, of U.S. Provisional Application No. 61/648,058, entitled, “COMPOSITIONS AND METHODS FOR MODULATING BDNF EXPRESSION”, filed on May 16, 2012, and of U.S. Provisional Application No. 61/648,051, entitled, “COMPOSITIONS AND METHODS FOR MODULATING MECP2 EXPRESSION”, filed on May 16, 2012, the contents of each of which are incorporated herein by reference in their entireties.

FIELD OF THE INVENTION

The invention relates to oligonucleotide based compositions, as well as methods of using oligonucleotide based compositions for treating disease.

BACKGROUND OF THE INVENTION

Transcriptome analyses have suggested that, although only 1-2% of the mammalian genome is protein coding, 70-90% is transcriptionally active. Recent discoveries argue that a subset of these non-protein coding transcripts play crucial roles in epigenetic regulation. In spite of their ubiquity, the structure and function of many of such transcripts remains uncharacterized. Recent studies indicate that some long non-coding RNAs function as an epigenetic regulator/RNA cofactor in chromatin remodeling through interactions with Polycomb repressor complex 2 (PRC2) and thus function to regulate gene expression.

SUMMARY OF THE INVENTION

Aspects of the invention provide methods for selecting oligonucleotides for activating or enhancing expression of target genes. The methods are particularly useful for identifying candidate oligonucleotides for activating or enhancing expression of target genes for which reduced expression or activity results in, or contributes to, disease. Further aspects of the invention provide methods of selecting a set of oligonucleotides that is enriched in oligonucleotides (e.g., compared with a random selection of oligonucleotides) that activate expression of a target gene. Accordingly, the methods may be used to establish large libraries of clinical candidates that are enriched in oligonucleotides that activate gene expression. Such libraries may be utilized, for example, to identify lead oligonucleotides for therapeutic development. Thus, the methods provided are useful for establishing a broad platform of candidate oligonucleotides for targeting the expression of most known genes, including protein coding genes. Further aspects provide single stranded oligonucleotides that modulate gene expression, and compositions and kits comprising the same. Methods for modulating gene expression using the single stranded oligonucleotides are also provided.

In some aspects, the invention is a method for selecting a candidate oligonucleotide for activating expression of a target gene by selecting a PRC2-associated region within a first nucleotide sequence, wherein the first nucleotide sequence maps to a position in a first chromosome between 50 kilobases upstream of a 5′-end of the target gene and 50 kilobases downstream of a 3′-end of the target gene; determining a second nucleotide sequence that is complementary with at least 8 consecutive nucleotides of the PRC2-associated region; and selecting as the candidate oligonucleotide, a single stranded oligonucleotide comprising the second nucleotide sequence, wherein the oligonucleotide has at least one of following features: a) a sequence comprising 5′-X-Y-Z, wherein X is any nucleotide, Y is a nucleotide sequence of 6 nucleotides in length that is not a seed sequence of a human microRNA, and Z is a nucleotide sequence of 1 to 23 nucleotides in length, wherein X is anchored at the 5′ end of the oligonucleotide; b) a sequence that does not comprise three or more consecutive guanosine nucleotides; c) a sequence that has less than a threshold level of sequence identity with every sequence of nucleotides, of equivalent length to the second nucleotide sequence, that is between 50 kilobases upstream of a 5′-end of an off-target gene and 50 kilobases downstream of a 3′-end of the off-target gene; d) a sequence that is complementary to a PRC2-associated region that encodes an RNA that forms a secondary structure comprising at least two single stranded loops; and/or e) a sequence that has greater than 60% G-C content.

In some embodiments, the single stranded oligonucleotide has only one of features a), b), c), d), and e). In some embodiments, the single stranded oligonucleotide has at least two of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has at least three of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has at least four of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has each of features a), b), c), d), and e). In certain embodiments, the oligonucleotide has the sequence 5′X-Y-Z, in which the oligonucleotide is 8-50 nucleotides in length. In some embodiments, Y is a sequence selected from Table 3.

In another aspect the invention is a method of selecting a set of oligonucleotides that is enriched in oligonucleotides that activate expression of a target gene, by selecting a PRC2-associated region within a first nucleotide sequence that maps to a position in a first chromosome between 50 kilobases upstream of a 5′-end of the target gene and 50 kilobases downstream of a 3′-end of the target gene; selecting a set of oligonucleotides, wherein each oligonucleotide in the set comprises a second nucleotide sequence that is complementary with at least 8 consecutive nucleotides of the PRC2-associated region, and has at least one of the following features: a) a sequence: 5′-X-Y-Z, wherein X is any nucleotide, Y is a nucleotide sequence of 6 nucleotides in length that is not a human seed sequence of a microRNA, and Z is a nucleotide sequence of 1 to 23 nucleotides in length, wherein X is anchored at the 5′ end of the oligonucleotide; b) a sequence that does not comprise three or more consecutive guanosine nucleotides; c) a sequence that has less than a threshold level of sequence identity with every sequence of nucleotides, of equivalent length to the second nucleotide sequence, that are between 50 kilobases upstream of a 5′-end of an off-target gene and 50 kilobases downstream of a 3′-end of the off-target gene; d) a sequence that is complementary to a PRC2-associated region that encodes an RNA that forms a secondary structure comprising at least two single stranded loops; and/or) a sequence that has greater than 60% G-C content; and wherein the set of oligonucleotides is enriched in oligonucleotides that activate expression of a target gene.

In some embodiments, each of the oligonucleotides has only one of features a), b), c), d), and e). In some embodiments, each of the oligonucleotides has at least two of features a), b), c), d), and e), each independently selected. In some embodiments, each of the oligonucleotides has at least three of features a), b), c), d), and e), each independently selected. In some embodiments, each of the oligonucleotides has at least four of features a), b), c), d), and e), each independently selected. In some embodiments, each of the oligonucleotides has each of features a), b), c), d), and e). In certain embodiments, each of the oligonucleotides has the sequence 5′X-Y-Z, in which the oligonucleotide is 8-50 nucleotides in length. In some embodiments, Y is a sequence selected from Table 3.

In some embodiments the single stranded oligonucleotide or each of the oligonucleotides is up to 100, 50, 40, 30, or 20 nucleotides in length. In other embodiments the single stranded oligonucleotide or each of the oligonucleotides is 8 to 30 nucleotides in length.

The threshold level of sequence identity in some embodiments is 50%, 60%, 70%, 80%, 85%, 90%, 95% or 99% sequence identity.

In one embodiment Y is a nucleotide sequence of 6 nucleotides in length set forth in Table 3.

In other embodiments the first chromosome is a chromosome of a first species, and wherein the method further comprises determining that the second nucleotide sequence is complementary to a second region of a second chromosome of a second species, the second region being located between 50 kilobases upstream of a 5′-end of a homolog of the target gene and 50 kilobases downstream of a 3′-end of the homolog of the target gene.

The second nucleotide sequence may be at least 80% complementary to the second region of the second chromosome

In some embodiments the first nucleotide sequence maps to the strand of the first chromosome comprising the sense strand of the target gene. In other embodiments the first nucleotide sequence maps to the strand of the first chromosome comprising the antisense strand of the target gene.

In some embodiments the PRC2-associated region is upstream of the 5′ end of the target gene and in other embodiments the PRC2-associated region is downstream of the 3′ end of the target gene. Optionally, the PRC2-associated region may be within an intron or an exon of the target gene or the PRC2-associated region may traverse an intron-exon junction, a 5′-UTR-exon junction or a 3′-UTR-exon junction of the target gene.

The PRC2-associated region may encode an RNA that forms a secondary structure comprising at least two single stranded loops. Optionally the secondary structure comprises a double stranded stem between the at least two single stranded loops. In some embodiments the at least 8 consecutive nucleotides of the PRC2-associated region encode at least a portion of at least one or at least two of the loops or at least a portion of the double stranded stem.

In other aspects the invention is a single stranded oligonucleotide comprising a region of complementarity that is complementary with at least 8 consecutive nucleotides of a PRC2-associated region located in a first chromosome between 50 kilobases upstream of a 5′-end of a target gene and 50 kilobases downstream of a 3′-end of the target gene, wherein the oligonucleotide has at least one of: a) a sequence comprising 5′-X-Y-Z, wherein X is any nucleotide, Y is a nucleotide sequence of 6 nucleotides in length that is not a human seed sequence of a microRNA, and Z is a nucleotide sequence of 1 to 23 nucleotides in length; b) a sequence that does not comprise three or more consecutive guanosine nucleotides; c) a sequence that has less than a threshold level of sequence identity with every sequence of nucleotides, of equivalent length to the second nucleotide sequence, that are between 50 kilobases upstream of a 5′-end of an off-target gene and 50 kilobases downstream of a 3′-end of the off-target gene; d) a sequence that is complementary to a PRC2-associated region that encodes an RNA that forms a secondary structure comprising at least two single stranded loops; and/or e) a sequence that has greater than 60% G-C content. In some embodiments, the single stranded oligonucleotide has only one of features a), b), c), d), and e). In some embodiments, the single stranded oligonucleotide has at least two of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has at least three of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has at least four of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has each of features a), b), c), d), and e). In certain embodiments, the oligonucleotide has the sequence 5′X-Y-Z, in which the oligonucleotide is 8-50 nucleotides in length. In some embodiments, Y is a sequence selected from Table 3.

The first chromosome is a chromosome of a first species in some embodiments. A sequence comprising the at least 8 consecutive nucleotides is located in a second chromosome between 50 kilobases upstream of a 5′-end of a homolog of the target gene and 50 kilobases downstream of a 3′-end of the homolog of the target gene, wherein the second chromosome is a chromosome of second species. The first species may be human and the second species may be a mouse.

The invention also includes a single stranded oligonucleotide of 8-30 nucleotides in length, wherein the single stranded oligonucleotide is complementary with at least 8 consecutive nucleotides of a PRC2-associated region located in a chromosome between 50 kilobases upstream of a 5′-end of a target gene and 50 kilobases downstream of a 3′-end of the target gene, wherein the nucleotide sequence of the single stranded oligonucleotide comprises one or more nucleotide sequences selected from (X)Xxxxxx, (X)xXxxxx, (X)xxXxxx, (X)xxxXxx, (X)xxxxXx and (X)xxxxxX, (X)XXxxxx, (X)XxXxxx, (X)XxxXxx, (X)XxxxXx, (X)XxxxxX, (X)xXXxxx, (X)xXxXxx, (X)xXxxXx, (X)xXxxxX, (X)xxXXxx, (X)xxXxXx, (X)xxXxxX, (X)xxxXXx, (X)xxxXxX and (X)xxxxXX, (X)XXXxxx, (X)xXXXxx, (X)xxXXXx, (X)xxxXXX, (X)XXxXxx, (X)XXxxXx, (X)XXxxxX, (X)xXXxXx, (X)xXXxxX, (X)xxXXxX, (X)XxXXxx, (X)XxxXXx (X)XxxxXX, (X)xXxXXx, (X)xXxxXX, (X)xxXxXX, (X)xXxXxX and (X)XxXxXx, (X)xxXXX, (X)xXxXXX, (X)xXXxXX, (X)xXXXxX, (X)xXXXXx, (X)XxxXXXX, (X)XxXxXX, (X)XxXXxX, (X)XxXXx, (X)XXxxXX, (X)XXxXxX, (X)XXxXXx, (X)XXXxxX, (X)XXXxXx, and (X)XXXXxx, (X)xXXXXX, (X)XxXXXX, (X)XXxXXX, (X)XXXxXX, (X)XXXXxX and (X)XXXXXx, and XXXXXX, XxXXXXX, XXxXXXX, XXXxXXX, XXXXxXX, XXXXXxX and XXXXXXx, wherein “X” denotes a nucleotide analogue, (X) denotes an optional nucleotide analogue, and “x” denotes a DNA or RNA nucleotide unit.

A single stranded oligonucleotide of 8 to 30 nucleotides in length having a region of complementarity that is complementary with at least 8 contiguous nucleotides of a long non-coding RNA (lncRNA) that regulates expression of a target gene, wherein 2-19 nucleotides of the oligonucleotide are nucleotide analogues is provided in other aspects of the invention.

In other aspects, a single stranded oligonucleotide of 5 to 30 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a long non-coding RNA (lncRNA) that regulates expression of a target gene, wherein the oligonucleotide is linked to a second oligonucleotide by a cleavable linker is provided. In some embodiments the oligonucleotide has the structure of any of the single stranded oligonucleotides described herein.

A single stranded single stranded oligonucleotide of 8 to 40 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a PRC2-binding long non-coding RNA (lncRNA) that regulates expression of a protein-coding reference gene, wherein the lncRNA is transcribed from the opposite strand as the protein-coding reference gene in a genomic region containing the protein-coding reference gene, wherein the single stranded oligonucleotide binds to a region of the lncRNA that originates within or overlaps an exon, an intron, exon, intron-exon junction, 5′ UTR, 3′ UTR, a translation initiation region, or a translation termination region is provided in other aspects of the invention.

A single stranded oligonucleotide of 8 to 40 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a long non-coding RNA (lncRNA) that regulates expression of a target gene is provided in other aspects of the invention. The oligonucleotide has complementarity to the lncRNA in a region of the lncRNA that is outside of the transcribed region of the target gene.

In yet other aspects of the invention a single stranded oligonucleotide of 8 to 30 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a long non-coding RNA (lncRNA) that inhibits expression of a target gene, wherein the oligonucleotide has complementarity to the lncRNA in a region of the lncRNA that is transcribed from a non-coding portion of the target gene is provided.

In some embodiments the lncRNA is a PRC2-associated region.

The present application incorporates by reference the nucleotide sequences listed as SEQ ID NOs:1-193,049 in International Patent Application PCT/US2011/060493, filed on Nov. 12, 2011, published on May 18, 2012, as WO/2012/065143, and entitled, “POLYCOMB-ASSOCIATED NON-CODING RNAS.” These sequences are referred to herein by their sequence identifier number preceded by an “A”. Accordingly, the set of nucleotide sequences incorporated by reference from International Patent Application PCT/US2011/060493 is referred to as “sequences A1-A193,049.”

The present application also incorporates by reference the nucleotide sequences listed as SEQ ID NOs: 1 to 916,209, or 916,626 to 934,931 in International Patent Application PCT/US2011/65939, filed on Dec. 19, 2011, published on Jun. 28, 2012, as WO/2012/087983, and entitled “POLYCOMB-ASSOCIATED NON-CODING RNAS.” These sequences are referred to herein by their sequence identifier number preceded by an “B”. Accordingly, the set of nucleotide sequences incorporated by reference from International Patent Application PCT/US2011/65939 is referred to as “sequences B1 to B916,209, or B916,626 to B934,931.”

In some embodiments the PRC2-associated region has a nucleotide sequence selected from sequences A1 to A193,049, B1 to B916,209, and B916,626 to B934,931.

In some embodiments, the PRC2-associated region has a nucleotide sequence selected from SEQ ID NO: 1-1212.

The oligonucleotide may be any length. In some embodiments the oligonucleotide is up to 100, 50, 40, 30, or 20 nucleotides in length. In other embodiments the oligonucleotide is 8 to 30 nucleotides in length. In yet other embodiments the oligonucleotide is 8 to 10 nucleotides in length and all but 1, 2, or 3 of the nucleotides of the complementary sequence of the PRC2-associated region are cytosine or guanosine nucleotides.

The at least 8 consecutive nucleotides of the PRC2-associated region in some embodiments is in the strand of the chromosome comprising the antisense strand of the target gene and in other embodiments is in the strand of the chromosome comprising the sense strand of the target gene.

In some embodiments the PRC2-associated region is upstream of the 5′ end of the target gene and in other embodiments the PRC2-associated region is downstream of the 3′ end of the target gene. Optionally, the PRC2-associated region may be within an intron or an exon of the target gene or the PRC2-associated region may traverse an intron-exon junction, a 5′-UTR-exon junction or a 3′-UTR-exon junction of the target gene.

The PRC2-associated region may encode an RNA that forms a secondary structure comprising at least two single stranded loops. Optionally the secondary structure comprises a double stranded stem between the at least two single stranded loops. In some embodiments the at least 8 consecutive nucleotides of the PRC2-associated region encode at least a portion of at least one or at least two of the loops or at least a portion of the double stranded stem.

In some embodiments the at least one nucleotide analogue results in an increase in T_(m) of the oligonucleotide in a range of 1 to 5° C. compared with an oligonucleotide that does not have the at least one nucleotide analogue.

In some embodiments at least one nucleotide of the oligonucleotide comprises a nucleotide analogue. In other embodiments each nucleotide of the oligonucleotide comprises a nucleotide analogue For instance the nucleotide analogue may be a 2′ O-methyl or a bridged nucleotide. In other embodiments the oligonucleotide comprises at least one ribonucleotide, at least one deoxyribonucleotide, or at least one bridged nucleotide. The bridged nucleotide may be, for instance, a LNA nucleotide, a cEt nucleotide or a ENA nucleotide analogue. Optionally each nucleotide of the oligonucleotide is a LNA nucleotide.

In some embodiments the nucleotides of the oligonucleotide comprise alternating nucleotide types. For instance, in some embodiments the oligonucleotide comprises deoxyribonucleotides and 2′-fluoro-deoxyribonucleotides. In other embodiments the nucleotides of the oligonucleotide comprise alternating deoxyribonucleotides and 2′-O-methyl nucleotides. In yet other embodiments the nucleotides of the oligonucleotide comprise alternating deoxyribonucleotides and ENA nucleotide analogues or the nucleotides of the oligonucleotide comprise alternating deoxyribonucleotides and LNA nucleotides. In yet other embodiments the nucleotides of the oligonucleotide comprise alternating LNA nucleotides and 2′-O-methyl nucleotides.

The 5′ nucleotide of the oligonucleotide may have different properties. For instance in some embodiments the 5′ nucleotide of the oligonucleotide is a deoxyribonucleotide or a LNA nucleotide.

In some embodiments the nucleotides of the oligonucleotide comprise deoxyribonucleotides flanked by at least one LNA nucleotide on each of the 5′ and 3′ ends of the deoxyribonucleotides.

The single stranded oligonucleotide may also include phosphorothioate internucleotide linkages between at least two nucleotides or between all nucleotides.

In some embodiments the nucleotide at the 3′ position of the oligonucleotide has a 3′ hydroxyl group. In other embodiments the nucleotide at the 3′ position of the oligonucleotide has a 3′ thiophosphate.

Optionally the single stranded oligonucleotide has a biotin moiety conjugated to the 5′ or 3′ nucleotide. In some embodiments the single stranded oligonucleotide has one or more of the following conjugates to either the 5′ or 3′ nucleotide or both: cholesterol, Vitamin A, folate, sigma receptor ligands, aptamers, peptides, such as CPP, hydrophobic molecules, such as lipids, ASGPR or dynamic polyconjugates and variants thereof.

A composition is provided in another aspect. The composition is a single stranded oligonucleotide described herein and a carrier, a buffered solution, and/or a pharmaceutically acceptable carrier.

In some aspects the invention is a composition of a single stranded RNA oligonucleotide of 8 to 20 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a long non-coding RNA (lncRNA) that regulates expression of a target gene, wherein 2-19 nucleotides of the oligonucleotide are nucleotide analogues, formulated in a pharmaceutically acceptable carrier, wherein a complementary RNA oligonucleotide is not present in the composition.

In some embodiments the nucleotide analogues are selected from the group consisting of a bridged nucleotide, 2′ fluoro, and 2′O-methyl nucleotide. In other embodiments the bridged nucleotide is a LNA, ENA or cEt nucleotide.

The lncRNA may be transcribed from the opposite strand as the target gene in a genomic region containing the target gene.

In some embodiments the oligonucleotide has complementarity to the lncRNA in a region of the lncRNA that is transcribed from a non-coding portion of the target gene. In other embodiments the oligonucleotide has complementarity to the lncRNA in a region of the lncRNA that is outside of the transcribed region of the target gene.

A kit comprising a container housing any of the compositions is also provided.

In other aspects the invention is a method of increasing expression of a target gene in a cell, by delivering a single stranded oligonucleotide described herein into the cell.

A method of increasing levels of a target gene in a subject by administering a single stranded oligonucleotide described herein to the subject is provided in other aspects of the invention.

A method of treating a condition associated with decreased levels of a target gene in a subject by administering a single stranded oligonucleotide described herein to the subject is provided in yet other aspects of the invention.

A method of upregulating gene expression is provided in other aspects. The method involves contacting a cell with a single stranded RNA oligonucleotide of 8 to 30 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a long non-coding RNA (lncRNA) that inhibits expression of a target gene.

The following applications are incorporated herein by reference in their entireties International Patent Application: PCT/US2011/65939, filed on Dec. 19, 2011, published on Jun. 28, 2012, as WO/2012/087983, and entitled POLYCOMB-ASSOCIATED NON-CODING RNAS, and International Patent Application: PCT/US2011/060493, filed on Nov. 12, 2011, published on May 18, 2012, as WO/2012/065143, and entitled POLYCOMB-ASSOCIATED NON-CODING RNAS.

Each of the limitations of the invention can encompass various embodiments of the invention. It is, therefore, anticipated that each of the limitations of the invention involving any one element or combinations of elements can be included in each aspect of the invention. This invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments and of being practiced or of being carried out in various ways. Also, the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting. The use of “including,” “comprising,” or “having,” “containing”, “involving”, and variations thereof herein, is meant to encompass the items listed thereafter and equivalents thereof as well as additional items.

TABLE 1 Brief Description of Sequence Listing Approx. SeqID Chrom gene Chr. Start Chr. End strand Organism Length 1 chr9 FXN 71638478 71705993 + Homo 67515 sapiens 2 chr9 FXN 71638478 71705993 − Homo 67515 sapiens 3 chr19 Fxn 24323942 24367076 − Mus 43134 musculus 4 chr19 Fxn 24323942 24367076 + Mus 43134 musculus 5 chr9 FXN 71651581 71651633 + Homo 52 sapiens 6 chr9 FXN 71651674 71651733 + Homo 59 sapiens 7 chr9 FXN 71664748 71664793 + Homo 45 sapiens 8 chr9 FXN 71676243 71676290 + Homo 47 sapiens 9 chr9 FXN 71677819 71678190 + Homo 371 sapiens 10 chr9 FXN 71649581 71653633 + Homo 4052 sapiens 11 chr9 FXN 71649674 71653733 + Homo 4059 sapiens 12 chr9 FXN 71662748 71666793 + Homo 4045 sapiens 13 chr9 FXN 71674243 71678290 + Homo 4047 sapiens 14 chr9 FXN 71675819 71680190 + Homo 4371 sapiens 15 chr9 FXN 71661444 71661499 − Homo 55 sapiens 16 chr9 FXN 71679886 71679910 − Homo 24 sapiens 17 chr9 FXN 71659444 71663499 − Homo 4055 sapiens 18 chr9 FXN 71677886 71681910 − Homo 4024 sapiens 19 chr5 SMN1 70208768 70260842 + Homo 52070 sapiens 20 chr5 SMN2 69333350 69385422 + Homo 52073 sapiens 21 chr9 SMNP 20319406 20344375 + Homo 24970 sapiens 22 chr5 SMN1 70208768 70260838 − Homo 52071 sapiens 23 chr5 SMN2 69333350 69385422 − Homo 52073 sapiens 24 chr9 SMNP 20319406 20344375 − Homo 24970 sapiens 25 chr13 Smn1 100881160 100919653 + Mus 38494 musculus 26 chr13 Smn1 100881160 100919653 − Mus 38494 musculus 27 chr5 SMN1 70240095 70240127 + Homo 32 sapiens 27 chr5 SMN2 69364672 69364704 + Homo 32 sapiens 28 chr5 SMN1 70214393 70214822 + Homo 429 sapiens 28 chr5 SMN2 69338976 69339405 + Homo 429 sapiens 29 chr5 SMN1 70214064 70214108 + Homo 44 sapiens 29 chr5 SMN2 69338647 69338691 + Homo 44 sapiens 30 chr5 SMN1 70214276 70214317 + Homo 41 sapiens 30 chr5 SMN2 69338859 69338900 + Homo 41 sapiens 31 chr5 SMN1 70214445 70214472 + Homo 27 sapiens 31 chr5 SMN2 69339028 69339055 + Homo 27 sapiens 32 chr5 SMN1 70238095 70242127 + Homo 4032 sapiens 32 chr5 SMN2 69362672 69366704 + Homo 4032 sapiens 33 chr5 SMN1 70212393 70216822 + Homo 4429 sapiens 33 chr5 SMN2 69336976 69341405 + Homo 4429 sapiens 34 chr5 SMN1 70212064 70216108 + Homo 4044 sapiens 34 chr5 SMN2 69336647 69340691 + Homo 4044 sapiens 35 chr5 SMN1 70212276 70216317 + Homo 4041 sapiens 35 chr5 SMN2 69336859 69340900 + Homo 4041 sapiens 36 chr5 SMN1 70212445 70216472 + Homo 4027 sapiens 36 chr5 SMN2 69337028 69341055 + Homo 4027 sapiens 37 chr5 SMN1 70240510 70240551 − Homo 41 sapiens 37 chr5 SMN2 69365087 69365128 − Homo 41 sapiens 38 chr5 SMN1 70241924 70241968 − Homo 44 sapiens 38 chr5 SMN2 69366499 69366543 − Homo 44 sapiens 39 chr5 SMN1 70238510 70242551 − Homo 4041 sapiens 39 chr5 SMN2 69363087 69367128 − Homo 4041 sapiens 40 chr5 SMN1 70239924 70243968 − Homo 4044 sapiens 40 chr5 SMN2 69364499 69368543 − Homo 4044 sapiens 41 chr5 SMN1 70247831 70247845 + Homo 14 sapiens 41 chr5 SMN2 69372411 69372425 + Homo 14 sapiens 42 chr5 SMN2 69372402 69372845 + Homo 443 sapiens 43 chr6 UTRN 144600872 145186170 + Homo 585298 sapiens 44 chr6 UTRN 144600872 145186170 − Homo 585298 sapiens 45 chr10 Utrn 12089985 12593533 − Mus 503548 musculus 46 chr10 Utrn 12089985 12593533 + Mus 503548 musculus 47 chr6 UTRN 144610489 144610535 + Homo 46 sapiens 48 chr6 UTRN 144612994 144613040 + Homo 46 sapiens 49 chr6 UTRN 144614120 144614162 + Homo 42 sapiens 50 chr6 UTRN 144614968 144615021 + Homo 53 sapiens 51 chr6 UTRN 144618862 144618901 + Homo 39 sapiens 52 chr6 UTRN 144621690 144621714 + Homo 24 sapiens 53 chr6 UTRN 144625028 144625096 + Homo 68 sapiens 54 chr6 UTRN 144625129 144625174 + Homo 45 sapiens 55 chr6 UTRN 144625319 144625379 + Homo 60 sapiens 56 chr6 UTRN 144628965 144629011 + Homo 46 sapiens 57 chr6 UTRN 144633818 144633869 + Homo 51 sapiens 58 chr6 UTRN 144633933 144633968 + Homo 35 sapiens 59 chr6 UTRN 144658267 144658302 + Homo 35 sapiens 60 chr6 UTRN 144685087 144685140 + Homo 53 sapiens 61 chr6 UTRN 144695039 144695063 + Homo 24 sapiens 62 chr6 UTRN 144699670 144699699 + Homo 29 sapiens 63 chr6 UTRN 144704043 144704398 + Homo 355 sapiens 64 chr6 UTRN 144706312 144706345 + Homo 33 sapiens 65 chr6 UTRN 144706654 144706704 + Homo 50 sapiens 66 chr6 UTRN 144721683 144721738 + Homo 55 sapiens 67 chr6 UTRN 144722580 144722627 + Homo 47 sapiens 68 chr6 UTRN 144724848 144724889 + Homo 41 sapiens 69 chr6 UTRN 144727897 144727947 + Homo 50 sapiens 70 chr6 UTRN 144746408 144746448 + Homo 40 sapiens 71 chr6 UTRN 144749102 144749152 + Homo 50 sapiens 72 chr6 UTRN 144749948 144750026 + Homo 78 sapiens 73 chr6 UTRN 144750728 144750789 + Homo 61 sapiens 74 chr6 UTRN 144750789 144750853 + Homo 64 sapiens 75 chr6 UTRN 144757162 144757214 + Homo 52 sapiens 76 chr6 UTRN 144757214 144757274 + Homo 60 sapiens 77 chr6 UTRN 144758752 144758807 + Homo 55 sapiens 78 chr6 UTRN 144758807 144758864 + Homo 57 sapiens 79 chr6 UTRN 144761513 144761579 + Homo 66 sapiens 80 chr6 UTRN 144765456 144765506 + Homo 50 sapiens 81 chr6 UTRN 144768420 144768461 + Homo 41 sapiens 82 chr6 UTRN 144768737 144768764 + Homo 27 sapiens 83 chr6 UTRN 144772549 144772627 + Homo 78 sapiens 84 chr6 UTRN 144774960 144775001 + Homo 41 sapiens 85 chr6 UTRN 144779914 144779960 + Homo 46 sapiens 86 chr6 UTRN 144780026 144780070 + Homo 44 sapiens 87 chr6 UTRN 144780278 144780324 + Homo 46 sapiens 88 chr6 UTRN 144783879 144783933 + Homo 54 sapiens 89 chr6 UTRN 144783933 144783995 + Homo 62 sapiens 90 chr6 UTRN 144800953 144800999 + Homo 46 sapiens 91 chr6 UTRN 144802780 144802822 + Homo 42 sapiens 92 chr6 UTRN 144803427 144803473 + Homo 46 sapiens 93 chr6 UTRN 144803714 144803742 + Homo 28 sapiens 94 chr6 UTRN 144803774 144803849 + Homo 75 sapiens 95 chr6 UTRN 144806673 144806714 + Homo 41 sapiens 96 chr6 UTRN 144808684 144808739 + Homo 55 sapiens 97 chr6 UTRN 144808739 144808803 + Homo 64 sapiens 98 chr6 UTRN 144809834 144809881 + Homo 47 sapiens 99 chr6 UTRN 144811266 144811310 + Homo 44 sapiens 100 chr6 UTRN 144814476 144814522 + Homo 46 sapiens 101 chr6 UTRN 144815156 144815199 + Homo 43 sapiens 102 chr6 UTRN 144820469 144820529 + Homo 60 sapiens 103 chr6 UTRN 144832193 144832243 + Homo 50 sapiens 104 chr6 UTRN 144835120 144835166 + Homo 46 sapiens 105 chr6 UTRN 144835862 144835907 + Homo 45 sapiens 106 chr6 UTRN 144837423 144837465 + Homo 42 sapiens 107 chr6 UTRN 144837943 144837989 + Homo 46 sapiens 108 chr6 UTRN 144844263 144844304 + Homo 41 sapiens 109 chr6 UTRN 144858722 144858798 + Homo 76 sapiens 110 chr6 UTRN 144870778 144870817 + Homo 39 sapiens 111 chr6 UTRN 144871113 144871154 + Homo 41 sapiens 112 chr6 UTRN 144872123 144872165 + Homo 42 sapiens 113 chr6 UTRN 144872599 144872669 + Homo 70 sapiens 114 chr6 UTRN 144873625 144873662 + Homo 37 sapiens 115 chr6 UTRN 144875136 144875182 + Homo 46 sapiens 116 chr6 UTRN 144875895 144875938 + Homo 43 sapiens 117 chr6 UTRN 144886315 144886378 + Homo 63 sapiens 118 chr6 UTRN 144904604 144904645 + Homo 41 sapiens 119 chr6 UTRN 144905276 144905300 + Homo 24 sapiens 120 chr6 UTRN 144906334 144906358 + Homo 24 sapiens 121 chr6 UTRN 144907025 144907055 + Homo 30 sapiens 122 chr6 UTRN 144908864 144908908 + Homo 44 sapiens 123 chr6 UTRN 144909055 144909078 + Homo 23 sapiens 124 chr6 UTRN 144910040 144910085 + Homo 45 sapiens 125 chr6 UTRN 144918990 144919013 + Homo 23 sapiens 126 chr6 UTRN 144935390 144935427 + Homo 37 sapiens 127 chr6 UTRN 144938199 144938248 + Homo 49 sapiens 128 chr6 UTRN 144941446 144941489 + Homo 43 sapiens 129 chr6 UTRN 144941551 144941596 + Homo 45 sapiens 130 chr6 UTRN 144941700 144941748 + Homo 48 sapiens 131 chr6 UTRN 144941856 144941912 + Homo 56 sapiens 132 chr6 UTRN 144941912 144941988 + Homo 76 sapiens 133 chr6 UTRN 144942080 144942136 + Homo 56 sapiens 134 chr6 UTRN 144944667 144944712 + Homo 45 sapiens 135 chr6 UTRN 144945160 144945207 + Homo 47 sapiens 136 chr6 UTRN 144950918 144950987 + Homo 69 sapiens 137 chr6 UTRN 144952595 144952650 + Homo 55 sapiens 138 chr6 UTRN 144954758 144954804 + Homo 46 sapiens 139 chr6 UTRN 144960952 144960996 + Homo 44 sapiens 140 chr6 UTRN 144968386 144968438 + Homo 52 sapiens 141 chr6 UTRN 144981668 144981709 + Homo 41 sapiens 142 chr6 UTRN 144985026 144985072 + Homo 46 sapiens 143 chr6 UTRN 144999637 144999686 + Homo 49 sapiens 144 chr6 UTRN 144999750 144999785 + Homo 35 sapiens 145 chr6 UTRN 144999904 144999956 + Homo 52 sapiens 146 chr6 UTRN 145012224 145012561 + Homo 337 sapiens 147 chr6 UTRN 145017897 145017969 + Homo 72 sapiens 148 chr6 UTRN 145017978 145018021 + Homo 43 sapiens 149 chr6 UTRN 145019229 145019261 + Homo 32 sapiens 150 chr6 UTRN 145021232 145021278 + Homo 46 sapiens 151 chr6 UTRN 145021336 145021382 + Homo 46 sapiens 152 chr6 UTRN 145031285 145031331 + Homo 46 sapiens 153 chr6 UTRN 145038424 145038467 + Homo 43 sapiens 154 chr6 UTRN 145042706 145042751 + Homo 45 sapiens 155 chr6 UTRN 145047775 145047820 + Homo 45 sapiens 156 chr6 UTRN 145051549 145051592 + Homo 43 sapiens 157 chr6 UTRN 145061899 145061941 + Homo 42 sapiens 158 chr6 UTRN 145063569 145063615 + Homo 46 sapiens 159 chr6 UTRN 145069445 145069497 + Homo 52 sapiens 160 chr6 UTRN 145072959 145073005 + Homo 46 sapiens 161 chr6 UTRN 145079115 145079162 + Homo 47 sapiens 162 chr6 UTRN 145079204 145079271 + Homo 67 sapiens 163 chr6 UTRN 145080780 145080816 + Homo 36 sapiens 164 chr6 UTRN 145080843 145080885 + Homo 42 sapiens 165 chr6 UTRN 145081884 145081930 + Homo 46 sapiens 166 chr6 UTRN 145087734 145087827 + Homo 93 sapiens 167 chr6 UTRN 145087827 145087911 + Homo 84 sapiens 168 chr6 UTRN 145088046 145088124 + Homo 78 sapiens 169 chr6 UTRN 145088210 145088245 + Homo 35 sapiens 170 chr6 UTRN 145088678 145088723 + Homo 45 sapiens 171 chr6 UTRN 145090281 145090327 + Homo 46 sapiens 172 chr6 UTRN 145090884 145090934 + Homo 50 sapiens 173 chr6 UTRN 145093542 145093591 + Homo 49 sapiens 174 chr6 UTRN 145094155 145094199 + Homo 44 sapiens 175 chr6 UTRN 145096714 145096756 + Homo 42 sapiens 176 chr6 UTRN 145101237 145101284 + Homo 47 sapiens 177 chr6 UTRN 145101598 145101642 + Homo 44 sapiens 178 chr6 UTRN 145127145 145127194 + Homo 49 sapiens 179 chr6 UTRN 145127467 145127507 + Homo 40 sapiens 180 chr6 UTRN 145127866 145127929 + Homo 63 sapiens 181 chr6 UTRN 145128105 145128160 + Homo 55 sapiens 182 chr6 UTRN 145128415 145128460 + Homo 45 sapiens 183 chr6 UTRN 145132350 145132397 + Homo 47 sapiens 184 chr6 UTRN 145132917 145132974 + Homo 57 sapiens 185 chr6 UTRN 145133779 145133802 + Homo 23 sapiens 186 chr6 UTRN 145134097 145134169 + Homo 72 sapiens 187 chr6 UTRN 145134835 145134881 + Homo 46 sapiens 188 chr6 UTRN 145142034 145142135 + Homo 101 sapiens 189 chr6 UTRN 145142629 145142676 + Homo 47 sapiens 190 chr6 UTRN 145148750 145148806 + Homo 56 sapiens 191 chr6 UTRN 145149936 145149984 + Homo 48 sapiens 192 chr6 UTRN 145153900 145154300 + Homo 400 sapiens 193 chr6 UTRN 145154735 145154782 + Homo 47 sapiens 194 chr6 UTRN 145155438 145155468 + Homo 30 sapiens 195 chr6 UTRN 145156972 145157019 + Homo 47 sapiens 196 chr6 UTRN 145157440 145157555 + Homo 115 sapiens 197 chr6 UTRN 145157566 145157621 + Homo 55 sapiens 198 chr6 UTRN 145158149 145158194 + Homo 45 sapiens 199 chr6 UTRN 145160356 145160409 + Homo 53 sapiens 200 chr6 UTRN 145161881 145161927 + Homo 46 sapiens 201 chr6 UTRN 145167107 145167151 + Homo 44 sapiens 202 chr6 UTRN 145167205 145167243 + Homo 38 sapiens 203 chr6 UTRN 145168292 145168344 + Homo 52 sapiens 204 chr6 UTRN 145169033 145169085 + Homo 52 sapiens 205 chr6 UTRN 145169156 145169202 + Homo 46 sapiens 206 chr6 UTRN 145169270 145169315 + Homo 45 sapiens 207 chr6 UTRN 145171814 145171863 + Homo 49 sapiens 208 chr6 UTRN 145173631 145173718 + Homo 87 sapiens 209 chr6 UTRN 144608489 144612535 + Homo 4046 sapiens 210 chr6 UTRN 144610994 144615040 + Homo 4046 sapiens 211 chr6 UTRN 144612120 144616162 + Homo 4042 sapiens 212 chr6 UTRN 144612968 144617021 + Homo 4053 sapiens 213 chr6 UTRN 144616862 144620901 + Homo 4039 sapiens 214 chr6 UTRN 144619690 144623714 + Homo 4024 sapiens 215 chr6 UTRN 144623028 144627096 + Homo 4068 sapiens 216 chr6 UTRN 144623129 144627174 + Homo 4045 sapiens 217 chr6 UTRN 144623319 144627379 + Homo 4060 sapiens 218 chr6 UTRN 144626965 144631011 + Homo 4046 sapiens 219 chr6 UTRN 144631818 144635869 + Homo 4051 sapiens 220 chr6 UTRN 144631933 144635968 + Homo 4035 sapiens 221 chr6 UTRN 144656267 144660302 + Homo 4035 sapiens 222 chr6 UTRN 144683087 144687140 + Homo 4053 sapiens 223 chr6 UTRN 144693039 144697063 + Homo 4024 sapiens 224 chr6 UTRN 144697670 144701699 + Homo 4029 sapiens 225 chr6 UTRN 144702043 144706398 + Homo 4355 sapiens 226 chr6 UTRN 144704312 144708345 + Homo 4033 sapiens 227 chr6 UTRN 144704654 144708704 + Homo 4050 sapiens 228 chr6 UTRN 144719683 144723738 + Homo 4055 sapiens 229 chr6 UTRN 144720580 144724627 + Homo 4047 sapiens 230 chr6 UTRN 144722848 144726889 + Homo 4041 sapiens 231 chr6 UTRN 144725897 144729947 + Homo 4050 sapiens 232 chr6 UTRN 144744408 144748448 + Homo 4040 sapiens 233 chr6 UTRN 144747102 144751152 + Homo 4050 sapiens 234 chr6 UTRN 144747948 144752026 + Homo 4078 sapiens 235 chr6 UTRN 144748728 144752789 + Homo 4061 sapiens 236 chr6 UTRN 144748789 144752853 + Homo 4064 sapiens 237 chr6 UTRN 144755162 144759214 + Homo 4052 sapiens 238 chr6 UTRN 144755214 144759274 + Homo 4060 sapiens 239 chr6 UTRN 144756752 144760807 + Homo 4055 sapiens 240 chr6 UTRN 144756807 144760864 + Homo 4057 sapiens 241 chr6 UTRN 144759513 144763579 + Homo 4066 sapiens 242 chr6 UTRN 144763456 144767506 + Homo 4050 sapiens 243 chr6 UTRN 144766420 144770461 + Homo 4041 sapiens 244 chr6 UTRN 144766737 144770764 + Homo 4027 sapiens 245 chr6 UTRN 144770549 144774627 + Homo 4078 sapiens 246 chr6 UTRN 144772960 144777001 + Homo 4041 sapiens 247 chr6 UTRN 144777914 144781960 + Homo 4046 sapiens 248 chr6 UTRN 144778026 144782070 + Homo 4044 sapiens 249 chr6 UTRN 144778278 144782324 + Homo 4046 sapiens 250 chr6 UTRN 144781879 144785933 + Homo 4054 sapiens 251 chr6 UTRN 144781933 144785995 + Homo 4062 sapiens 252 chr6 UTRN 144798953 144802999 + Homo 4046 sapiens 253 chr6 UTRN 144800780 144804822 + Homo 4042 sapiens 254 chr6 UTRN 144801427 144805473 + Homo 4046 sapiens 255 chr6 UTRN 144801714 144805742 + Homo 4028 sapiens 256 chr6 UTRN 144801774 144805849 + Homo 4075 sapiens 257 chr6 UTRN 144804673 144808714 + Homo 4041 sapiens 258 chr6 UTRN 144806684 144810739 + Homo 4055 sapiens 259 chr6 UTRN 144806739 144810803 + Homo 4064 sapiens 260 chr6 UTRN 144807834 144811881 + Homo 4047 sapiens 261 chr6 UTRN 144809266 144813310 + Homo 4044 sapiens 262 chr6 UTRN 144812476 144816522 + Homo 4046 sapiens 263 chr6 UTRN 144813156 144817199 + Homo 4043 sapiens 264 chr6 UTRN 144818469 144822529 + Homo 4060 sapiens 265 chr6 UTRN 144830193 144834243 + Homo 4050 sapiens 266 chr6 UTRN 144833120 144837166 + Homo 4046 sapiens 267 chr6 UTRN 144833862 144837907 + Homo 4045 sapiens 268 chr6 UTRN 144835423 144839465 + Homo 4042 sapiens 269 chr6 UTRN 144835943 144839989 + Homo 4046 sapiens 270 chr6 UTRN 144842263 144846304 + Homo 4041 sapiens 271 chr6 UTRN 144856722 144860798 + Homo 4076 sapiens 272 chr6 UTRN 144868778 144872817 + Homo 4039 sapiens 273 chr6 UTRN 144869113 144873154 + Homo 4041 sapiens 274 chr6 UTRN 144870123 144874165 + Homo 4042 sapiens 275 chr6 UTRN 144870599 144874669 + Homo 4070 sapiens 276 chr6 UTRN 144871625 144875662 + Homo 4037 sapiens 277 chr6 UTRN 144873136 144877182 + Homo 4046 sapiens 278 chr6 UTRN 144873895 144877938 + Homo 4043 sapiens 279 chr6 UTRN 144884315 144888378 + Homo 4063 sapiens 280 chr6 UTRN 144902604 144906645 + Homo 4041 sapiens 281 chr6 UTRN 144903276 144907300 + Homo 4024 sapiens 282 chr6 UTRN 144904334 144908358 + Homo 4024 sapiens 283 chr6 UTRN 144905025 144909055 + Homo 4030 sapiens 284 chr6 UTRN 144906864 144910908 + Homo 4044 sapiens 285 chr6 UTRN 144907055 144911078 + Homo 4023 sapiens 286 chr6 UTRN 144908040 144912085 + Homo 4045 sapiens 287 chr6 UTRN 144916990 144921013 + Homo 4023 sapiens 288 chr6 UTRN 144933390 144937427 + Homo 4037 sapiens 289 chr6 UTRN 144936199 144940248 + Homo 4049 sapiens 290 chr6 UTRN 144939446 144943489 + Homo 4043 sapiens 291 chr6 UTRN 144939551 144943596 + Homo 4045 sapiens 292 chr6 UTRN 144939700 144943748 + Homo 4048 sapiens 293 chr6 UTRN 144939856 144943912 + Homo 4056 sapiens 294 chr6 UTRN 144939912 144943988 + Homo 4076 sapiens 295 chr6 UTRN 144940080 144944136 + Homo 4056 sapiens 296 chr6 UTRN 144942667 144946712 + Homo 4045 sapiens 297 chr6 UTRN 144943160 144947207 + Homo 4047 sapiens 298 chr6 UTRN 144948918 144952987 + Homo 4069 sapiens 299 chr6 UTRN 144950595 144954650 + Homo 4055 sapiens 300 chr6 UTRN 144952758 144956804 + Homo 4046 sapiens 301 chr6 UTRN 144958952 144962996 + Homo 4044 sapiens 302 chr6 UTRN 144966386 144970438 + Homo 4052 sapiens 303 chr6 UTRN 144979668 144983709 + Homo 4041 sapiens 304 chr6 UTRN 144983026 144987072 + Homo 4046 sapiens 305 chr6 UTRN 144997637 145001686 + Homo 4049 sapiens 306 chr6 UTRN 144997750 145001785 + Homo 4035 sapiens 307 chr6 UTRN 144997904 145001956 + Homo 4052 sapiens 308 chr6 UTRN 145010224 145014561 + Homo 4337 sapiens 309 chr6 UTRN 145015897 145019969 + Homo 4072 sapiens 310 chr6 UTRN 145015978 145020021 + Homo 4043 sapiens 311 chr6 UTRN 145017229 145021261 + Homo 4032 sapiens 312 chr6 UTRN 145019232 145023278 + Homo 4046 sapiens 313 chr6 UTRN 145019336 145023382 + Homo 4046 sapiens 314 chr6 UTRN 145029285 145033331 + Homo 4046 sapiens 315 chr6 UTRN 145036424 145040467 + Homo 4043 sapiens 316 chr6 UTRN 145040706 145044751 + Homo 4045 sapiens 317 chr6 UTRN 145045775 145049820 + Homo 4045 sapiens 318 chr6 UTRN 145049549 145053592 + Homo 4043 sapiens 319 chr6 UTRN 145059899 145063941 + Homo 4042 sapiens 320 chr6 UTRN 145061569 145065615 + Homo 4046 sapiens 321 chr6 UTRN 145067445 145071497 + Homo 4052 sapiens 322 chr6 UTRN 145070959 145075005 + Homo 4046 sapiens 323 chr6 UTRN 145077115 145081162 + Homo 4047 sapiens 324 chr6 UTRN 145077204 145081271 + Homo 4067 sapiens 325 chr6 UTRN 145078780 145082816 + Homo 4036 sapiens 326 chr6 UTRN 145078843 145082885 + Homo 4042 sapiens 327 chr6 UTRN 145079884 145083930 + Homo 4046 sapiens 328 chr6 UTRN 145085734 145089827 + Homo 4093 sapiens 329 chr6 UTRN 145085827 145089911 + Homo 4084 sapiens 330 chr6 UTRN 145086046 145090124 + Homo 4078 sapiens 331 chr6 UTRN 145086210 145090245 + Homo 4035 sapiens 332 chr6 UTRN 145086678 145090723 + Homo 4045 sapiens 333 chr6 UTRN 145088281 145092327 + Homo 4046 sapiens 334 chr6 UTRN 145088884 145092934 + Homo 4050 sapiens 335 chr6 UTRN 145091542 145095591 + Homo 4049 sapiens 336 chr6 UTRN 145092155 145096199 + Homo 4044 sapiens 337 chr6 UTRN 145094714 145098756 + Homo 4042 sapiens 338 chr6 UTRN 145099237 145103284 + Homo 4047 sapiens 339 chr6 UTRN 145099598 145103642 + Homo 4044 sapiens 340 chr6 UTRN 145125145 145129194 + Homo 4049 sapiens 341 chr6 UTRN 145125467 145129507 + Homo 4040 sapiens 342 chr6 UTRN 145125866 145129929 + Homo 4063 sapiens 343 chr6 UTRN 145126105 145130160 + Homo 4055 sapiens 344 chr6 UTRN 145126415 145130460 + Homo 4045 sapiens 345 chr6 UTRN 145130350 145134397 + Homo 4047 sapiens 346 chr6 UTRN 145130917 145134974 + Homo 4057 sapiens 347 chr6 UTRN 145131779 145135802 + Homo 4023 sapiens 348 chr6 UTRN 145132097 145136169 + Homo 4072 sapiens 349 chr6 UTRN 145132835 145136881 + Homo 4046 sapiens 350 chr6 UTRN 145140034 145144135 + Homo 4101 sapiens 351 chr6 UTRN 145140629 145144676 + Homo 4047 sapiens 352 chr6 UTRN 145146750 145150806 + Homo 4056 sapiens 353 chr6 UTRN 145147936 145151984 + Homo 4048 sapiens 354 chr6 UTRN 145151900 145156300 + Homo 4400 sapiens 355 chr6 UTRN 145152735 145156782 + Homo 4047 sapiens 356 chr6 UTRN 145153438 145157468 + Homo 4030 sapiens 357 chr6 UTRN 145154972 145159019 + Homo 4047 sapiens 358 chr6 UTRN 145155440 145159555 + Homo 4115 sapiens 359 chr6 UTRN 145155566 145159621 + Homo 4055 sapiens 360 chr6 UTRN 145156149 145160194 + Homo 4045 sapiens 361 chr6 UTRN 145158356 145162409 + Homo 4053 sapiens 362 chr6 UTRN 145159881 145163927 + Homo 4046 sapiens 363 chr6 UTRN 145165107 145169151 + Homo 4044 sapiens 364 chr6 UTRN 145165205 145169243 + Homo 4038 sapiens 365 chr6 UTRN 145166292 145170344 + Homo 4052 sapiens 366 chr6 UTRN 145167033 145171085 + Homo 4052 sapiens 367 chr6 UTRN 145167156 145171202 + Homo 4046 sapiens 368 chr6 UTRN 145167270 145171315 + Homo 4045 sapiens 369 chr6 UTRN 145169814 145173863 + Homo 4049 sapiens 370 chr6 UTRN 145171631 145175718 + Homo 4087 sapiens 371 chr6 UTRN 144608031 144608073 − Homo 42 sapiens 372 chr6 UTRN 144612926 144612972 − Homo 46 sapiens 373 chr6 UTRN 144628552 144628595 − Homo 43 sapiens 374 chr6 UTRN 144633946 144633970 − Homo 24 sapiens 375 chr6 UTRN 144650739 144650804 − Homo 65 sapiens 376 chr6 UTRN 144657045 144657093 − Homo 48 sapiens 377 chr6 UTRN 144696995 144697041 − Homo 46 sapiens 378 chr6 UTRN 144747612 144747674 − Homo 62 sapiens 379 chr6 UTRN 144747879 144747925 − Homo 46 sapiens 380 chr6 UTRN 144759816 144759863 − Homo 47 sapiens 381 chr6 UTRN 144768238 144768312 − Homo 74 sapiens 382 chr6 UTRN 144780036 144780082 − Homo 46 sapiens 383 chr6 UTRN 144782886 144782935 − Homo 49 sapiens 384 chr6 UTRN 144795766 144795789 − Homo 23 sapiens 385 chr6 UTRN 144806556 144806601 − Homo 45 sapiens 386 chr6 UTRN 144854365 144854401 − Homo 36 sapiens 387 chr6 UTRN 144858769 144858809 − Homo 40 sapiens 388 chr6 UTRN 144861763 144861805 − Homo 42 sapiens 389 chr6 UTRN 144865560 144865594 − Homo 34 sapiens 390 chr6 UTRN 144871095 144871118 − Homo 23 sapiens 391 chr6 UTRN 144872146 144872179 − Homo 33 sapiens 392 chr6 UTRN 144873792 144873815 − Homo 23 sapiens 393 chr6 UTRN 144875726 144875775 − Homo 49 sapiens 394 chr6 UTRN 144881389 144881429 − Homo 40 sapiens 395 chr6 UTRN 144902992 144903093 − Homo 101 sapiens 396 chr6 UTRN 144913242 144913292 − Homo 50 sapiens 397 chr6 UTRN 144916606 144916629 − Homo 23 sapiens 398 chr6 UTRN 144953033 144953075 − Homo 42 sapiens 399 chr6 UTRN 144957938 144957985 − Homo 47 sapiens 400 chr6 UTRN 144960849 144960900 − Homo 51 sapiens 401 chr6 UTRN 144963737 144963802 − Homo 65 sapiens 402 chr6 UTRN 144980957 144981000 − Homo 43 sapiens 403 chr6 UTRN 144981226 144981271 − Homo 45 sapiens 404 chr6 UTRN 144981350 144981396 − Homo 46 sapiens 405 chr6 UTRN 144981507 144981542 − Homo 35 sapiens 406 chr6 UTRN 144983660 144983707 − Homo 47 sapiens 407 chr6 UTRN 145005066 145005095 − Homo 29 sapiens 408 chr6 UTRN 145005500 145005548 − Homo 48 sapiens 409 chr6 UTRN 145021339 145021384 − Homo 45 sapiens 410 chr6 UTRN 145036068 145036136 − Homo 68 sapiens 411 chr6 UTRN 145036766 145036820 − Homo 54 sapiens 412 chr6 UTRN 145038552 145038606 − Homo 54 sapiens 413 chr6 UTRN 145058056 145058096 − Homo 40 sapiens 414 chr6 UTRN 145059402 145059450 − Homo 48 sapiens 415 chr6 UTRN 145060834 145060905 − Homo 71 sapiens 416 chr6 UTRN 145062448 145062475 − Homo 27 sapiens 417 chr6 UTRN 145063125 145063160 − Homo 35 sapiens 418 chr6 UTRN 145063273 145063302 − Homo 29 sapiens 419 chr6 UTRN 145071318 145071359 − Homo 41 sapiens 420 chr6 UTRN 145079495 145079543 − Homo 48 sapiens 421 chr6 UTRN 145090227 145090266 − Homo 39 sapiens 422 chr6 UTRN 145095420 145095465 − Homo 45 sapiens 423 chr6 UTRN 145097191 145097232 − Homo 41 sapiens 424 chr6 UTRN 145098097 145098128 − Homo 31 sapiens 425 chr6 UTRN 145098960 145099005 − Homo 45 sapiens 426 chr6 UTRN 145106983 145107024 − Homo 41 sapiens 427 chr6 UTRN 145124174 145124220 − Homo 46 sapiens 428 chr6 UTRN 145128278 145128325 − Homo 47 sapiens 429 chr6 UTRN 145142105 145142152 − Homo 47 sapiens 430 chr6 UTRN 145149926 145149972 − Homo 46 sapiens 431 chr6 UTRN 145153110 145153155 − Homo 45 sapiens 432 chr6 UTRN 145155586 145155641 − Homo 55 sapiens 433 chr6 UTRN 145156956 145157020 − Homo 64 sapiens 434 chr6 UTRN 145161886 145161931 − Homo 45 sapiens 435 chr6 UTRN 145166490 145166527 − Homo 37 sapiens 436 chr6 UTRN 145167701 145167736 − Homo 35 sapiens 437 chr6 UTRN 145173585 145173627 − Homo 42 sapiens 438 chr6 UTRN 144606031 144610073 − Homo 4042 sapiens 439 chr6 UTRN 144610926 144614972 − Homo 4046 sapiens 440 chr6 UTRN 144626552 144630595 − Homo 4043 sapiens 441 chr6 UTRN 144631946 144635970 − Homo 4024 sapiens 442 chr6 UTRN 144648739 144652804 − Homo 4065 sapiens 443 chr6 UTRN 144655045 144659093 − Homo 4048 sapiens 444 chr6 UTRN 144694995 144699041 − Homo 4046 sapiens 445 chr6 UTRN 144745612 144749674 − Homo 4062 sapiens 446 chr6 UTRN 144745879 144749925 − Homo 4046 sapiens 447 chr6 UTRN 144757816 144761863 − Homo 4047 sapiens 448 chr6 UTRN 144766238 144770312 − Homo 4074 sapiens 449 chr6 UTRN 144778036 144782082 − Homo 4046 sapiens 450 chr6 UTRN 144780886 144784935 − Homo 4049 sapiens 451 chr6 UTRN 144793766 144797789 − Homo 4023 sapiens 452 chr6 UTRN 144804556 144808601 − Homo 4045 sapiens 453 chr6 UTRN 144852365 144856401 − Homo 4036 sapiens 454 chr6 UTRN 144856769 144860809 − Homo 4040 sapiens 455 chr6 UTRN 144859763 144863805 − Homo 4042 sapiens 456 chr6 UTRN 144863560 144867594 − Homo 4034 sapiens 457 chr6 UTRN 144869095 144873118 − Homo 4023 sapiens 458 chr6 UTRN 144870146 144874179 − Homo 4033 sapiens 459 chr6 UTRN 144871792 144875815 − Homo 4023 sapiens 460 chr6 UTRN 144873726 144877775 − Homo 4049 sapiens 461 chr6 UTRN 144879389 144883429 − Homo 4040 sapiens 462 chr6 UTRN 144900992 144905093 − Homo 4101 sapiens 463 chr6 UTRN 144911242 144915292 − Homo 4050 sapiens 464 chr6 UTRN 144914606 144918629 − Homo 4023 sapiens 465 chr6 UTRN 144951033 144955075 − Homo 4042 sapiens 466 chr6 UTRN 144955938 144959985 − Homo 4047 sapiens 467 chr6 UTRN 144958849 144962900 − Homo 4051 sapiens 468 chr6 UTRN 144961737 144965802 − Homo 4065 sapiens 469 chr6 UTRN 144978957 144983000 − Homo 4043 sapiens 470 chr6 UTRN 144979226 144983271 − Homo 4045 sapiens 471 chr6 UTRN 144979350 144983396 − Homo 4046 sapiens 472 chr6 UTRN 144979507 144983542 − Homo 4035 sapiens 473 chr6 UTRN 144981660 144985707 − Homo 4047 sapiens 474 chr6 UTRN 145003066 145007095 − Homo 4029 sapiens 475 chr6 UTRN 145003500 145007548 − Homo 4048 sapiens 476 chr6 UTRN 145019339 145023384 − Homo 4045 sapiens 477 chr6 UTRN 145034068 145038136 − Homo 4068 sapiens 478 chr6 UTRN 145034766 145038820 − Homo 4054 sapiens 479 chr6 UTRN 145036552 145040606 − Homo 4054 sapiens 480 chr6 UTRN 145056056 145060096 − Homo 4040 sapiens 481 chr6 UTRN 145057402 145061450 − Homo 4048 sapiens 482 chr6 UTRN 145058834 145062905 − Homo 4071 sapiens 483 chr6 UTRN 145060448 145064475 − Homo 4027 sapiens 484 chr6 UTRN 145061125 145065160 − Homo 4035 sapiens 485 chr6 UTRN 145061273 145065302 − Homo 4029 sapiens 486 chr6 UTRN 145069318 145073359 − Homo 4041 sapiens 487 chr6 UTRN 145077495 145081543 − Homo 4048 sapiens 488 chr6 UTRN 145088227 145092266 − Homo 4039 sapiens 489 chr6 UTRN 145093420 145097465 − Homo 4045 sapiens 490 chr6 UTRN 145095191 145099232 − Homo 4041 sapiens 491 chr6 UTRN 145096097 145100128 − Homo 4031 sapiens 492 chr6 UTRN 145096960 145101005 − Homo 4045 sapiens 493 chr6 UTRN 145104983 145109024 − Homo 4041 sapiens 494 chr6 UTRN 145122174 145126220 − Homo 4046 sapiens 495 chr6 UTRN 145126278 145130325 − Homo 4047 sapiens 496 chr6 UTRN 145140105 145144152 − Homo 4047 sapiens 497 chr6 UTRN 145147926 145151972 − Homo 4046 sapiens 498 chr6 UTRN 145151110 145155155 − Homo 4045 sapiens 499 chr6 UTRN 145153586 145157641 − Homo 4055 sapiens 500 chr6 UTRN 145154956 145159020 − Homo 4064 sapiens 501 chr6 UTRN 145159886 145163931 − Homo 4045 sapiens 502 chr6 UTRN 145164490 145168527 − Homo 4037 sapiens 503 chr6 UTRN 145165701 145169736 − Homo 4035 sapiens 504 chr6 UTRN 145171585 145175627 − Homo 4042 sapiens 505 chr11 HBB 5234695 5260301 − Homo 25606 sapiens 506 chr11 HBB 5234695 5260301 + Homo 25606 sapiens 507 chr11 HBD 5242058 5267858 − Homo 25800 sapiens 508 chr11 HBD 5242058 5267858 + Homo 25800 sapiens 509 chr11 HBE1 5277579 5303373 − Homo 25794 sapiens 510 chr11 HBE1 5277579 5303373 + Homo 25794 sapiens 511 chr11 HBG1 5257501 5283087 − Homo 25586 sapiens 512 chr11 HBG1 5257501 5283087 + Homo 25586 sapiens 513 chr11 HBG2 5262420 5288011 − Homo 25591 sapiens 514 chr11 HBG2 5262420 5288011 + Homo 25591 sapiens 515 chr7 Hbb-b1 110949041 110974437 − Mus 25396 musculus 516 chr7 Hbb-b1 110949041 110974437 + Mus 25396 musculus 517 chr7 Hbb-bh1 110978151 111003676 − Mus 25525 musculus 518 chr7 Hbb-bh1 110978151 111003676 + Mus 25525 musculus 519 chr7 Hbb-y 110988267 111013721 − Mus 25454 musculus 520 chr7 Hbb-y 110988267 111013721 + Mus 25454 musculus 521 chr11 HBB/HBD 5246366 5246414 + Homo 48 sapiens 522 chr11 HBB/HBD 5244366 5248414 + Homo 4048 sapiens 523 chr12 ATP2A2 110707031 110800897 + Homo 93866 sapiens 524 chr12 ATP2A2 110707031 110800897 − Homo 93866 sapiens 525 chr5 Atp2a2 122891521 122964234 − Mus 72713 musculus 526 chr5 Atp2a2 122891521 122964234 + Mus 72713 musculus 527 chr12 ATP2A2 110719627 110719694 + Homo 67 sapiens 528 chr12 ATP2A2 110720529 110720579 + Homo 50 sapiens 529 chr12 ATP2A2 110721473 110721523 + Homo 50 sapiens 530 chr12 ATP2A2 110723314 110723392 + Homo 78 sapiens 531 chr12 ATP2A2 110725261 110725324 + Homo 63 sapiens 532 chr12 ATP2A2 110727087 110727134 + Homo 47 sapiens 533 chr12 ATP2A2 110729885 110729930 + Homo 45 sapiens 534 chr12 ATP2A2 110734433 110734479 + Homo 46 sapiens 535 chr12 ATP2A2 110764013 110764059 + Homo 46 sapiens 536 chr12 ATP2A2 110765378 110765425 + Homo 47 sapiens 537 chr12 ATP2A2 110765494 110765540 + Homo 46 sapiens 538 chr12 ATP2A2 110765734 110765819 + Homo 85 sapiens 539 chr12 ATP2A2 110770988 110771034 + Homo 46 sapiens 540 chr12 ATP2A2 110771832 110771877 + Homo 45 sapiens 541 chr12 ATP2A2 110777332 110777374 + Homo 42 sapiens 542 chr12 ATP2A2 110777482 110777528 + Homo 46 sapiens 543 chr12 ATP2A2 110778549 110778580 + Homo 31 sapiens 544 chr12 ATP2A2 110778678 110778748 + Homo 70 sapiens 545 chr12 ATP2A2 110780135 110780183 + Homo 48 sapiens 546 chr12 ATP2A2 110780320 110780386 + Homo 66 sapiens 547 chr12 ATP2A2 110781060 110781169 + Homo 109 sapiens 548 chr12 ATP2A2 110781169 110781235 + Homo 66 sapiens 549 chr12 ATP2A2 110782732 110782779 + Homo 47 sapiens 550 chr12 ATP2A2 110783060 110783131 + Homo 71 sapiens 551 chr12 ATP2A2 110783131 110783186 + Homo 55 sapiens 552 chr12 ATP2A2 110783143 110783843 + Homo 700 sapiens 553 chr12 ATP2A2 110783803 110783845 + Homo 42 sapiens 554 chr12 ATP2A2 110784061 110784090 + Homo 29 sapiens 555 chr12 ATP2A2 110784453 110784505 + Homo 52 sapiens 556 chr12 ATP2A2 110784577 110784623 + Homo 46 sapiens 557 chr12 ATP2A2 110784786 110784835 + Homo 49 sapiens 558 chr12 ATP2A2 110784919 110784969 + Homo 50 sapiens 559 chr12 ATP2A2 110788463 110788513 + Homo 50 sapiens 560 chr12 ATP2A2 110717627 110721694 + Homo 4067 sapiens 561 chr12 ATP2A2 110718529 110722579 + Homo 4050 sapiens 562 chr12 ATP2A2 110719473 110723523 + Homo 4050 sapiens 563 chr12 ATP2A2 110721314 110725392 + Homo 4078 sapiens 564 chr12 ATP2A2 110723261 110727324 + Homo 4063 sapiens 565 chr12 ATP2A2 110725087 110729134 + Homo 4047 sapiens 566 chr12 ATP2A2 110727885 110731930 + Homo 4045 sapiens 567 chr12 ATP2A2 110732433 110736479 + Homo 4046 sapiens 568 chr12 ATP2A2 110762013 110766059 + Homo 4046 sapiens 569 chr12 ATP2A2 110763378 110767425 + Homo 4047 sapiens 570 chr12 ATP2A2 110763494 110767540 + Homo 4046 sapiens 571 chr12 ATP2A2 110763734 110767819 + Homo 4085 sapiens 572 chr12 ATP2A2 110768988 110773034 + Homo 4046 sapiens 573 chr12 ATP2A2 110769832 110773877 + Homo 4045 sapiens 574 chr12 ATP2A2 110775332 110779374 + Homo 4042 sapiens 575 chr12 ATP2A2 110775482 110779528 + Homo 4046 sapiens 576 chr12 ATP2A2 110776549 110780580 + Homo 4031 sapiens 577 chr12 ATP2A2 110776678 110780748 + Homo 4070 sapiens 578 chr12 ATP2A2 110778135 110782183 + Homo 4048 sapiens 579 chr12 ATP2A2 110778320 110782386 + Homo 4066 sapiens 580 chr12 ATP2A2 110779060 110783169 + Homo 4109 sapiens 581 chr12 ATP2A2 110779169 110783235 + Homo 4066 sapiens 582 chr12 ATP2A2 110780732 110784779 + Homo 4047 sapiens 583 chr12 ATP2A2 110781060 110785131 + Homo 4071 sapiens 584 chr12 ATP2A2 110781131 110785186 + Homo 4055 sapiens 585 chr12 ATP2A2 110781143 110785843 + Homo 4700 sapiens 586 chr12 ATP2A2 110781803 110785845 + Homo 4042 sapiens 587 chr12 ATP2A2 110782061 110786090 + Homo 4029 sapiens 588 chr12 ATP2A2 110782453 110786505 + Homo 4052 sapiens 589 chr12 ATP2A2 110782577 110786623 + Homo 4046 sapiens 590 chr12 ATP2A2 110782786 110786835 + Homo 4049 sapiens 591 chr12 ATP2A2 110782919 110786969 + Homo 4050 sapiens 592 chr12 ATP2A2 110786463 110790513 + Homo 4050 sapiens 593 chr12 ATP2A2 110764239 110764284 − Homo 45 sapiens 594 chr12 ATP2A2 110771869 110771910 − Homo 41 sapiens 595 chr12 ATP2A2 110777311 110777357 − Homo 46 sapiens 596 chr12 ATP2A2 110778603 110778648 − Homo 45 sapiens 597 chr12 ATP2A2 110781134 110781180 − Homo 46 sapiens 598 chr12 ATP2A2 110783112 110783161 − Homo 49 sapiens 599 chr12 ATP2A2 110783116 110783161 − Homo 45 sapiens 600 chr12 ATP2A2 110784019 110784061 − Homo 42 sapiens 601 chr12 ATP2A2 110784142 110784184 − Homo 42 sapiens 602 chr12 ATP2A2 110762239 110766284 − Homo 4045 sapiens 603 chr12 ATP2A2 110769869 110773910 − Homo 4041 sapiens 604 chr12 ATP2A2 110775311 110779357 − Homo 4046 sapiens 605 chr12 ATP2A2 110776603 110780648 − Homo 4045 sapiens 606 chr12 ATP2A2 110779134 110783180 − Homo 4046 sapiens 607 chr12 ATP2A2 110781112 110785161 − Homo 4049 sapiens 608 chr12 ATP2A2 110781116 110785161 − Homo 4045 sapiens 609 chr12 ATP2A2 110782019 110786061 − Homo 4042 sapiens 610 chr12 ATP2A2 110782142 110786184 − Homo 4042 sapiens 611 chr11 APOA1 116694468 116720338 − Homo 25870 sapiens 612 chr11 APOA1 116694468 116720338 + Homo 25870 sapiens 613 chr4 Abca1 53031660 53184767 − Mus 153107 musculus 614 chr4 Abca1 53031660 53184767 + Mus 153107 musculus 615 chr9 ABCA1 107531283 107702527 − Homo 171244 sapiens 616 chr9 ABCA1 107531283 107702527 + Homo 171244 sapiens 617 chr9 Apoa1 46024712 46050549 + Mus 25837 musculus 618 chr9 Apoa1 46024712 46050549 − Mus 25837 musculus 619 chr11 APOA1 116703452 116703490 − Homo 38 sapiens 620 chr11 APOA1 116716006 116716043 − Homo 37 sapiens 621 chr9 ABCA1 107544853 107544898 − Homo 45 sapiens 622 chr9 ABCA1 107545317 107545373 − Homo 56 sapiens 623 chr9 ABCA1 107549175 107549221 − Homo 46 sapiens 624 chr9 ABCA1 107550274 107550320 − Homo 46 sapiens 625 chr9 ABCA1 107550704 107550746 − Homo 42 sapiens 626 chr9 ABCA1 107550769 107550815 − Homo 46 sapiens 627 chr9 ABCA1 107553424 107553449 − Homo 25 sapiens 628 chr9 ABCA1 107555135 107555180 − Homo 45 sapiens 629 chr9 ABCA1 107559478 107559514 − Homo 36 sapiens 630 chr9 ABCA1 107562144 107562189 − Homo 45 sapiens 631 chr9 ABCA1 107562811 107562856 − Homo 45 sapiens 632 chr9 ABCA1 107564383 107564429 − Homo 46 sapiens 633 chr9 ABCA1 107564542 107564589 − Homo 47 sapiens 634 chr9 ABCA1 107565573 107565597 − Homo 24 sapiens 635 chr9 ABCA1 107566955 107566997 − Homo 42 sapiens 636 chr9 ABCA1 107567799 107567822 − Homo 23 sapiens 637 chr9 ABCA1 107568594 107568642 − Homo 48 sapiens 638 chr9 ABCA1 107570966 107571012 − Homo 46 sapiens 639 chr9 ABCA1 107571761 107571807 − Homo 46 sapiens 640 chr9 ABCA1 107572492 107572538 − Homo 46 sapiens 641 chr9 ABCA1 107573100 107573151 − Homo 51 sapiens 642 chr9 ABCA1 107574024 107574054 − Homo 30 sapiens 643 chr9 ABCA1 107574852 107574906 − Homo 54 sapiens 644 chr9 ABCA1 107574906 107574968 − Homo 62 sapiens 645 chr9 ABCA1 107576399 107576466 − Homo 67 sapiens 646 chr9 ABCA1 107576708 107576754 − Homo 46 sapiens 647 chr9 ABCA1 107578270 107578349 − Homo 79 sapiens 648 chr9 ABCA1 107578369 107578447 − Homo 78 sapiens 649 chr9 ABCA1 107582257 107582303 − Homo 46 sapiens 650 chr9 ABCA1 107583704 107583756 − Homo 52 sapiens 651 chr9 ABCA1 107584821 107584867 − Homo 46 sapiens 652 chr9 ABCA1 107590239 107590277 − Homo 38 sapiens 653 chr9 ABCA1 107590789 107590834 − Homo 45 sapiens 654 chr9 ABCA1 107591342 107591392 − Homo 50 sapiens 655 chr9 ABCA1 107593256 107593298 − Homo 42 sapiens 656 chr9 ABCA1 107593396 107593433 − Homo 37 sapiens 657 chr9 ABCA1 107593922 107593967 − Homo 45 sapiens 658 chr9 ABCA1 107594977 107595047 − Homo 70 sapiens 659 chr9 ABCA1 107596375 107596423 − Homo 48 sapiens 660 chr9 ABCA1 107597784 107597829 − Homo 45 sapiens 661 chr9 ABCA1 107597907 107597985 − Homo 78 sapiens 662 chr9 ABCA1 107602215 107602260 − Homo 45 sapiens 663 chr9 ABCA1 107602653 107602701 − Homo 48 sapiens 664 chr9 ABCA1 107613685 107613749 − Homo 64 sapiens 665 chr9 ABCA1 107615130 107615165 − Homo 35 sapiens 666 chr9 ABCA1 107620268 107620352 − Homo 84 sapiens 667 chr9 ABCA1 107620400 107620445 − Homo 45 sapiens 668 chr9 ABCA1 107624149 107624175 − Homo 26 sapiens 669 chr9 ABCA1 107625349 107625393 − Homo 44 sapiens 670 chr9 ABCA1 107632152 107632259 − Homo 107 sapiens 671 chr9 ABCA1 107640145 107640188 − Homo 43 sapiens 672 chr9 ABCA1 107648733 107648779 − Homo 46 sapiens 673 chr9 ABCA1 107651606 107651651 − Homo 45 sapiens 674 chr9 ABCA1 107651838 107651884 − Homo 46 sapiens 675 chr9 ABCA1 107654768 107654818 − Homo 50 sapiens 676 chr9 ABCA1 107656823 107656846 − Homo 23 sapiens 677 chr9 ABCA1 107663411 107663449 − Homo 38 sapiens 678 chr9 ABCA1 107664297 107664344 − Homo 47 sapiens 679 chr9 ABCA1 107666346 107666399 − Homo 53 sapiens 680 chr9 ABCA1 107666418 107666515 − Homo 97 sapiens 681 chr9 ABCA1 107669296 107669353 − Homo 57 sapiens 682 chr9 ABCA1 107669453 107669501 − Homo 48 sapiens 683 chr9 ABCA1 107669654 107669754 − Homo 100 sapiens 684 chr9 ABCA1 107669789 107669837 − Homo 48 sapiens 685 chr9 ABCA1 107688863 107688904 − Homo 41 sapiens 686 chr9 ABCA1 107689641 107689696 − Homo 55 sapiens 687 chr9 ABCA1 107689892 107689938 − Homo 46 sapiens 688 chr9 ABCA1 107690078 107690126 − Homo 48 sapiens 689 chr9 ABCA1 107690345 107690386 − Homo 41 sapiens 690 chr11 ABCA1 116701452 116705490 − Homo 4038 sapiens 691 chr11 ABCA1 116714006 116718043 − Homo 4037 sapiens 692 chr9 ABCA1 107542853 107546898 − Homo 4045 sapiens 693 chr9 ABCA1 107543317 107547373 − Homo 4056 sapiens 694 chr9 ABCA1 107547175 107551221 − Homo 4046 sapiens 695 chr9 ABCA1 107548274 107552320 − Homo 4046 sapiens 696 chr9 ABCA1 107548704 107552746 − Homo 4042 sapiens 697 chr9 ABCA1 107548769 107552815 − Homo 4046 sapiens 698 chr9 ABCA1 107551424 107555449 − Homo 4025 sapiens 699 chr9 ABCA1 107553135 107557180 − Homo 4045 sapiens 700 chr9 ABCA1 107557478 107561514 − Homo 4036 sapiens 701 chr9 ABCA1 107560144 107564189 − Homo 4045 sapiens 702 chr9 ABCA1 107560811 107564856 − Homo 4045 sapiens 703 chr9 ABCA1 107562383 107566429 − Homo 4046 sapiens 704 chr9 ABCA1 107562542 107566589 − Homo 4047 sapiens 705 chr9 ABCA1 107563573 107567597 − Homo 4024 sapiens 706 chr9 ABCA1 107564955 107568997 − Homo 4042 sapiens 707 chr9 ABCA1 107565799 107569822 − Homo 4023 sapiens 708 chr9 ABCA1 107566594 107570642 − Homo 4048 sapiens 709 chr9 ABCA1 107568966 107573012 − Homo 4046 sapiens 710 chr9 ABCA1 107569761 107573807 − Homo 4046 sapiens 711 chr9 ABCA1 107570492 107574538 − Homo 4046 sapiens 712 chr9 ABCA1 107571100 107575151 − Homo 4051 sapiens 713 chr9 ABCA1 107572024 107576054 − Homo 4030 sapiens 714 chr9 ABCA1 107572852 107576906 − Homo 4054 sapiens 715 chr9 ABCA1 107572906 107576968 − Homo 4062 sapiens 716 chr9 ABCA1 107574399 107578466 − Homo 4067 sapiens 717 chr9 ABCA1 107574708 107578754 − Homo 4046 sapiens 718 chr9 ABCA1 107576270 107580349 − Homo 4079 sapiens 719 chr9 ABCA1 107576369 107580447 − Homo 4078 sapiens 720 chr9 ABCA1 107580257 107584303 − Homo 4046 sapiens 721 chr9 ABCA1 107581704 107585756 − Homo 4052 sapiens 722 chr9 ABCA1 107582821 107586867 − Homo 4046 sapiens 723 chr9 ABCA1 107588239 107592277 − Homo 4038 sapiens 724 chr9 ABCA1 107588789 107592834 − Homo 4045 sapiens 725 chr9 ABCA1 107589342 107593392 − Homo 4050 sapiens 726 chr9 ABCA1 107591256 107595298 − Homo 4042 sapiens 727 chr9 ABCA1 107591396 107595433 − Homo 4037 sapiens 728 chr9 ABCA1 107591922 107595967 − Homo 4045 sapiens 729 chr9 ABCA1 107592977 107597047 − Homo 4070 sapiens 730 chr9 ABCA1 107594375 107598423 − Homo 4048 sapiens 731 chr9 ABCA1 107595784 107599829 − Homo 4045 sapiens 732 chr9 ABCA1 107595907 107599985 − Homo 4078 sapiens 733 chr9 ABCA1 107600215 107604260 − Homo 4045 sapiens 734 chr9 ABCA1 107600653 107604701 − Homo 4048 sapiens 735 chr9 ABCA1 107611685 107615749 − Homo 4064 sapiens 736 chr9 ABCA1 107613130 107617165 − Homo 4035 sapiens 737 chr9 ABCA1 107618268 107622352 − Homo 4084 sapiens 738 chr9 ABCA1 107618400 107622445 − Homo 4045 sapiens 739 chr9 ABCA1 107622149 107626175 − Homo 4026 sapiens 740 chr9 ABCA1 107623349 107627393 − Homo 4044 sapiens 741 chr9 ABCA1 107630152 107634259 − Homo 4107 sapiens 742 chr9 ABCA1 107638145 107642188 − Homo 4043 sapiens 743 chr9 ABCA1 107646733 107650779 − Homo 4046 sapiens 744 chr9 ABCA1 107649606 107653651 − Homo 4045 sapiens 745 chr9 ABCA1 107649838 107653884 − Homo 4046 sapiens 746 chr9 ABCA1 107652768 107656818 − Homo 4050 sapiens 747 chr9 ABCA1 107654823 107658846 − Homo 4023 sapiens 748 chr9 ABCA1 107661411 107665449 − Homo 4038 sapiens 749 chr9 ABCA1 107662297 107666344 − Homo 4047 sapiens 750 chr9 ABCA1 107664346 107668399 − Homo 4053 sapiens 751 chr9 ABCA1 107664418 107668515 − Homo 4097 sapiens 752 chr9 ABCA1 107667296 107671353 − Homo 4057 sapiens 753 chr9 ABCA1 107667453 1076715 − Homo 4048 sapiens 754 chr9 ABCA1 107667654 107671754 − Homo 4100 sapiens 755 chr9 ABCA1 107667789 107671837 − Homo 4048 sapiens 756 chr9 ABCA1 107686863 107690904 − Homo 4041 sapiens 757 chr9 ABCA1 107687641 107691696 − Homo 4055 sapiens 758 chr9 ABCA1 107687892 107691938 − Homo 4046 sapiens 759 chr9 ABCA1 107688078 107692126 − Homo 4048 sapiens 760 chr9 ABCA1 107688345 107692386 − Homo 4041 sapiens 761 chr11 ABCA1 116707870 116707947 + Homo 77 sapiens 762 chr11 ABCA1 116714416 116714458 + Homo 42 sapiens 763 chr11 ABCA1 116714536 116714578 + Homo 42 sapiens 764 chr11 ABCA1 116714762 116714821 + Homo 59 sapiens 765 chr9 ABCA1 107535234 107535273 + Homo 39 sapiens 766 chr9 ABCA1 107544880 107544926 + Homo 46 sapiens 767 chr9 ABCA1 107547830 107547871 + Homo 41 sapiens 768 chr9 ABCA1 107555512 107555554 + Homo 42 sapiens 769 chr9 ABCA1 107565561 107565603 + Homo 42 sapiens 770 chr9 ABCA1 107573103 107573142 + Homo 39 sapiens 771 chr9 ABCA1 107599184 107599234 + Homo 50 sapiens 772 chr9 ABCA1 107601126 107601170 + Homo 44 sapiens 773 chr9 ABCA1 107607774 107607819 + Homo 45 sapiens 774 chr9 ABCA1 107613720 107613783 + Homo 63 sapiens 775 chr9 ABCA1 107623957 107624003 + Homo 46 sapiens 776 chr9 ABCA1 107630025 107630076 + Homo 51 sapiens 777 chr9 ABCA1 107631197 107631265 + Homo 68 sapiens 778 chr9 ABCA1 107633948 107633996 + Homo 48 sapiens 779 chr9 ABCA1 107648816 107648890 + Homo 74 sapiens 780 chr9 ABCA1 107650500 107650558 + Homo 58 sapiens 781 chr9 ABCA1 107665550 107665591 + Homo 41 sapiens 782 chr9 ABCA1 107666033 107666073 + Homo 40 sapiens 783 chr11 ABCA1 116705870 116709947 + Homo 4077 sapiens 784 chr11 ABCA1 116712416 116716458 + Homo 4042 sapiens 785 chr11 ABCA1 116712536 116716578 + Homo 4042 sapiens 786 chr11 ABCA1 116712762 116716821 + Homo 4059 sapiens 787 chr9 ABCA1 107533234 107537273 + Homo 4039 sapiens 788 chr9 ABCA1 107542880 107546926 + Homo 4046 sapiens 789 chr9 ABCA1 107545830 107549871 + Homo 4041 sapiens 790 chr9 ABCA1 107553512 107557554 + Homo 4042 sapiens 791 chr9 ABCA1 107563561 107567603 + Homo 4042 sapiens 792 chr9 ABCA1 107571103 107575142 + Homo 4039 sapiens 793 chr9 ABCA1 107597184 107601234 + Homo 4050 sapiens 794 chr9 ABCA1 107599126 107603170 + Homo 4044 sapiens 795 chr9 ABCA1 107605774 107609819 + Homo 4045 sapiens 796 chr9 ABCA1 107611720 107615783 + Homo 4063 sapiens 797 chr9 ABCA1 107621957 107626003 + Homo 4046 sapiens 798 chr9 ABCA1 107628025 107632076 + Homo 4051 sapiens 799 chr9 ABCA1 107629197 107633265 + Homo 4068 sapiens 800 chr9 ABCA1 107631948 107635996 + Homo 4048 sapiens 801 chr9 ABCA1 107646816 107650890 + Homo 4074 sapiens 802 chr9 ABCA1 107648500 107652558 + Homo 4058 sapiens 803 chr9 ABCA1 107663550 107667591 + Homo 4041 sapiens 804 chr9 ABCA1 107664033 107668073 + Homo 4040 sapiens 805 chr10 PTEN 89611194 89740532 + Homo 129338 sapiens 806 chr10 PTEN 89611194 89740532 − Homo 129338 sapiens 807 chr19 Pten 32820066 32912650 + Mus 92584 musculus 808 chr19 Pten 32820066 32912650 − Mus 92584 musculus 809 chr10 PTEN 89624228 89624270 + Homo 42 sapiens 810 chr10 PTEN 89624833 89624878 + Homo 45 sapiens 811 chr10 PTEN 89624926 89624970 + Homo 44 sapiens 812 chr10 PTEN 89625394 89625442 + Homo 48 sapiens 813 chr10 PTEN 89625544 89625602 + Homo 58 sapiens 814 chr10 PTEN 89625817 89625863 + Homo 46 sapiens 815 chr10 PTEN 89625913 89625938 + Homo 25 sapiens 816 chr10 PTEN 89625981 89626027 + Homo 46 sapiens 817 chr10 PTEN 89626204 89626244 + Homo 40 sapiens 818 chr10 PTEN 89626597 89626641 + Homo 44 sapiens 819 chr10 PTEN 89626724 89626775 + Homo 51 sapiens 820 chr10 PTEN 89626875 89626911 + Homo 36 sapiens 821 chr10 PTEN 89627125 89627169 + Homo 44 sapiens 822 chr10 PTEN 89628194 89628243 + Homo 49 sapiens 823 chr10 PTEN 89630898 89630936 + Homo 38 sapiens 824 chr10 PTEN 89633768 89633831 + Homo 63 sapiens 825 chr10 PTEN 89637731 89637778 + Homo 47 sapiens 826 chr10 PTEN 89655949 89655994 + Homo 45 sapiens 827 chr10 PTEN 89685417 89685446 + Homo 29 sapiens 828 chr10 PTEN 89686532 89686579 + Homo 47 sapiens 829 chr10 PTEN 89686846 89686893 + Homo 47 sapiens 830 chr10 PTEN 89690160 89690213 + Homo 53 sapiens 831 chr10 PTEN 89691658 89691701 + Homo 43 sapiens 832 chr10 PTEN 89692927 89692973 + Homo 46 sapiens 833 chr10 PTEN 89693941 89693990 + Homo 49 sapiens 834 chr10 PTEN 89695260 89695313 + Homo 53 sapiens 835 chr10 PTEN 89695827 89695873 + Homo 46 sapiens 836 chr10 PTEN 89697310 89697355 + Homo 45 sapiens 837 chr10 PTEN 89698069 89698110 + Homo 41 sapiens 838 chr10 PTEN 89698500 89698543 + Homo 43 sapiens 839 chr10 PTEN 89698790 89698828 + Homo 38 sapiens 840 chr10 PTEN 89699611 89699656 + Homo 45 sapiens 841 chr10 PTEN 89700446 89700493 + Homo 47 sapiens 842 chr10 PTEN 89700876 89700919 + Homo 43 sapiens 843 chr10 PTEN 89701325 89701377 + Homo 52 sapiens 844 chr10 PTEN 89701617 89701717 + Homo 100 sapiens 845 chr10 PTEN 89701764 89701818 + Homo 54 sapiens 846 chr10 PTEN 89701915 89701962 + Homo 47 sapiens 847 chr10 PTEN 89712065 89712111 + Homo 46 sapiens 848 chr10 PTEN 89712351 89712402 + Homo 51 sapiens 849 chr10 PTEN 89712411 89712510 + Homo 99 sapiens 850 chr10 PTEN 89714201 89714228 + Homo 27 sapiens 851 chr10 PTEN 89717191 89717238 + Homo 47 sapiens 852 chr10 PTEN 89720717 89720765 + Homo 48 sapiens 853 chr10 PTEN 89723393 89723443 + Homo 50 sapiens 854 chr10 PTEN 89725518 89725564 + Homo 46 sapiens 855 chr10 PTEN 89725617 89725658 + Homo 41 sapiens 856 chr10 PTEN 89725819 89725865 + Homo 46 sapiens 857 chr10 PTEN 89726333 89726368 + Homo 35 sapiens 858 chr10 PTEN 89726640 89726709 + Homo 69 sapiens 859 chr10 PTEN 89727525 89727567 + Homo 42 sapiens 860 chr10 PTEN 89727527 89727569 + Homo 42 sapiens 861 chr10 PTEN 89728125 89728171 + Homo 46 sapiens 862 chr10 PTEN 89728126 89728170 + Homo 44 sapiens 863 chr10 PTEN 89728128 89728172 + Homo 44 sapiens 864 chr10 PTEN 89730064 89730112 + Homo 48 sapiens 865 chr10 PTEN 89730269 89730384 + Homo 115 sapiens 866 chr10 PTEN 89622228 89626270 + Homo 4042 sapiens 867 chr10 PTEN 89622833 89626878 + Homo 4045 sapiens 868 chr10 PTEN 89622926 89626970 + Homo 4044 sapiens 869 chr10 PTEN 89623394 89627442 + Homo 4048 sapiens 870 chr10 PTEN 89623544 89627602 + Homo 4058 sapiens 871 chr10 PTEN 89623817 89627863 + Homo 4046 sapiens 872 chr10 PTEN 89623913 89627938 + Homo 4025 sapiens 873 chr10 PTEN 89623981 89628027 + Homo 4046 sapiens 874 chr10 PTEN 89624204 89628244 + Homo 4040 sapiens 875 chr10 PTEN 89624597 89628641 + Homo 4044 sapiens 876 chr10 PTEN 89624724 89628775 + Homo 4051 sapiens 877 chr10 PTEN 89624875 89628911 + Homo 4036 sapiens 878 chr10 PTEN 89625125 89629169 + Homo 4044 sapiens 879 chr10 PTEN 89626194 89630243 + Homo 4049 sapiens 880 chr10 PTEN 89628898 89632936 + Homo 4038 sapiens 881 chr10 PTEN 89631768 89635831 + Homo 4063 sapiens 882 chr10 PTEN 89635731 89639778 + Homo 4047 sapiens 883 chr10 PTEN 89653949 89657994 + Homo 4045 sapiens 884 chr10 PTEN 89683417 89687446 + Homo 4029 sapiens 885 chr10 PTEN 89684532 89688579 + Homo 4047 sapiens 886 chr10 PTEN 89684846 89688893 + Homo 4047 sapiens 887 chr10 PTEN 89688160 89692213 + Homo 4053 sapiens 888 chr10 PTEN 89689658 89693701 + Homo 4043 sapiens 889 chr10 PTEN 89690927 89694973 + Homo 4046 sapiens 890 chr10 PTEN 89691941 89695990 + Homo 4049 sapiens 891 chr10 PTEN 89693260 89697313 + Homo 4053 sapiens 892 chr10 PTEN 89693827 89697873 + Homo 4046 sapiens 893 chr10 PTEN 89695310 89699355 + Homo 4045 sapiens 894 chr10 PTEN 89696069 89700110 + Homo 4041 sapiens 895 chr10 PTEN 89696500 89700543 + Homo 4043 sapiens 896 chr10 PTEN 89696790 89700828 + Homo 4038 sapiens 897 chr10 PTEN 89697611 89701656 + Homo 4045 sapiens 898 chr10 PTEN 89698446 89702493 + Homo 4047 sapiens 899 chr10 PTEN 89698876 89702919 + Homo 4043 sapiens 900 chr10 PTEN 89699325 89703377 + Homo 4052 sapiens 901 chr10 PTEN 89699617 89703717 + Homo 4100 sapiens 902 chr10 PTEN 89699764 89703818 + Homo 4054 sapiens 903 chr10 PTEN 89699915 89703962 + Homo 4047 sapiens 904 chr10 PTEN 89710065 89714111 + Homo 4046 sapiens 905 chr10 PTEN 89710351 89714402 + Homo 4051 sapiens 906 chr10 PTEN 89710411 89714510 + Homo 4099 sapiens 907 chr10 PTEN 89712201 89716228 + Homo 4027 sapiens 908 chr10 PTEN 89715191 89719238 + Homo 4047 sapiens 909 chr10 PTEN 89718717 89722765 + Homo 4048 sapiens 910 chr10 PTEN 89721393 89725443 + Homo 4050 sapiens 911 chr10 PTEN 89723518 89727564 + Homo 4046 sapiens 912 chr10 PTEN 89723617 89727658 + Homo 4041 sapiens 913 chr10 PTEN 89723819 89727865 + Homo 4046 sapiens 914 chr10 PTEN 89724333 89728368 + Homo 4035 sapiens 915 chr10 PTEN 89724640 89728709 + Homo 4069 sapiens 916 chr10 PTEN 89725525 89729567 + Homo 4042 sapiens 917 chr10 PTEN 89725527 89729569 + Homo 4042 sapiens 918 chr10 PTEN 89726125 89730171 + Homo 4046 sapiens 919 chr10 PTEN 89726126 89730170 + Homo 4044 sapiens 920 chr10 PTEN 89726128 89730172 + Homo 4044 sapiens 921 chr10 PTEN 89728064 89732112 + Homo 4048 sapiens 922 chr10 PTEN 89728269 89732384 + Homo 4115 sapiens 923 chr10 PTEN 89623576 89623622 − Homo 46 sapiens 924 chr10 PTEN 89623906 89623956 − Homo 50 sapiens 925 chr10 PTEN 89624031 89624073 − Homo 42 sapiens 926 chr10 PTEN 89624202 89624247 − Homo 45 sapiens 927 chr10 PTEN 89624760 89624805 − Homo 45 sapiens 928 chr10 PTEN 89625073 89625113 − Homo 40 sapiens 929 chr10 PTEN 89628887 89628953 − Homo 66 sapiens 930 chr10 PTEN 89665539 89665573 − Homo 34 sapiens 931 chr10 PTEN 89692964 89693006 − Homo 42 sapiens 932 chr10 PTEN 89695528 89695586 − Homo 58 sapiens 933 chr10 PTEN 89695765 89695876 − Homo 111 sapiens 934 chr10 PTEN 89695889 89695911 − Homo 22 sapiens 935 chr10 PTEN 89697361 89697418 − Homo 57 sapiens 936 chr10 PTEN 89697767 89697812 − Homo 45 sapiens 937 chr10 PTEN 89721856 89721896 − Homo 40 sapiens 938 chr10 PTEN 89621576 89625622 − Homo 4046 sapiens 939 chr10 PTEN 89621906 89625956 − Homo 4050 sapiens 940 chr10 PTEN 89622031 89626073 − Homo 4042 sapiens 941 chr10 PTEN 89622202 89626247 − Homo 4045 sapiens 942 chr10 PTEN 89622760 89626805 − Homo 4045 sapiens 943 chr10 PTEN 89623073 89627113 − Homo 4040 sapiens 944 chr10 PTEN 89626887 89630953 − Homo 4066 sapiens 945 chr10 PTEN 89663539 89667573 − Homo 4034 sapiens 946 chr10 PTEN 89690964 89695006 − Homo 4042 sapiens 947 chr10 PTEN 89693528 89697586 − Homo 4058 sapiens 948 chr10 PTEN 89693765 89697876 − Homo 4111 sapiens 949 chr10 PTEN 89693889 89697911 − Homo 4022 sapiens 950 chr10 PTEN 89695361 89699418 − Homo 4057 sapiens 951 chr10 PTEN 89695767 89699812 − Homo 4045 sapiens 952 chr10 PTEN 89719856 89723896 − Homo 4040 sapiens 953 chr11 BDNF 27664441 27693196 − Homo 28755 sapiens 954 chr11 BDNF 27664441 27693196 + Homo 28755 sapiens 955 chr11 BDNF-AS1 27516398 27731718 + Homo 215320 sapiens 956 chr11 BDNF-AS1 27516398 27731718 − Homo 215320 sapiens 957 chr2 Bdnf 109502856 109579200 + Mus 76344 musculus 958 chr2 Bdnf 109502856 109579200 − Mus 76344 musculus 959 chr11 BDNF 27678819 27678888 − Homo 69 sapiens 960 chr11 BDNF 27679423 27679469 − Homo 46 sapiens 961 chr11 BDNF 27679512 27679558 − Homo 46 sapiens 962 chr11 BDNF 27679705 27679749 − Homo 44 sapiens 963 chr11 BDNF 27686657 27686742 − Homo 85 sapiens 964 chr11 BDNF 27718502 27718548 − Homo 46 sapiens 965 chr11 BDNF 27719743 27719780 − Homo 37 sapiens 966 chr11 BDNF 27721391 27721434 − Homo 43 sapiens 967 chr11 BDNF 27676819 27680888 − Homo 4069 sapiens 968 chr11 BDNF 27677423 27681469 − Homo 4046 sapiens 969 chr11 BDNF 27677512 27681558 − Homo 4046 sapiens 970 chr11 BDNF 27677705 27681749 − Homo 4044 sapiens 971 chr11 BDNF 27684657 27688742 − Homo 4085 sapiens 972 chr11 BDNF 27716502 27720548 − Homo 4046 sapiens 973 chr11 BDNF 27717743 27721780 − Homo 4037 sapiens 974 chr11 BDNF 27719391 27723434 − Homo 4043 sapiens 975 chr11 BDNF 27739230 27739276 − Homo 46 sapiens 976 chr11 BDNF 27741576 27741622 − Homo 46 sapiens 977 chr11 BDNF 27742481 27742526 − Homo 45 sapiens 978 chr11 BDNF 27742552 27742602 − Homo 50 sapiens 979 chr11 BDNF 27737230 27741276 − Homo 4046 sapiens 980 chr11 BDNF 27739576 27743622 − Homo 4046 sapiens 981 chr11 BDNF 27740481 27744526 − Homo 4045 sapiens 982 chr11 BDNF 27740552 27744602 − Homo 4050 sapiens 983 chr11 BDNF 27518527 27518574 − Homo 47 sapiens 984 chr11 BDNF 27518780 27518823 − Homo 43 sapiens 985 chr11 BDNF 27518870 27518922 − Homo 52 sapiens 986 chr11 BDNF 27519285 27519333 − Homo 48 sapiens 987 chr11 BDNF 27520498 27520547 − Homo 49 sapiens 988 chr11 BDNF 27520913 27520996 − Homo 83 sapiens 989 chr11 BDNF 27521081 27521112 − Homo 31 sapiens 990 chr11 BDNF 27523348 27523395 − Homo 47 sapiens 991 chr11 BDNF 27523423 27523469 − Homo 46 sapiens 992 chr11 BDNF 27516527 27520574 − Homo 4047 sapiens 993 chr11 BDNF 27516780 27520823 − Homo 4043 sapiens 994 chr11 BDNF 27516870 27520922 − Homo 4052 sapiens 995 chr11 BDNF 27517285 27521333 − Homo 4048 sapiens 996 chr11 BDNF 27518498 27522547 − Homo 4049 sapiens 997 chr11 BDNF 27518913 27522996 − Homo 4083 sapiens 998 chr11 BDNF 27519081 27523112 − Homo 4031 sapiens 999 chr11 BDNF 27521348 27525395 − Homo 4047 sapiens 1000 chr11 BDNF 27521423 27525469 − Homo 4046 sapiens 1001 chr11 BDNF 27681917 27681964 + Homo 47 sapiens 1002 chr11 BDNF 27697978 27698023 + Homo 45 sapiens 1003 chr11 BDNF 27718599 27718680 + Homo 81 sapiens 1004 chr11 BDNF 27679917 27683964 + Homo 4047 sapiens 1005 chr11 BDNF 27695978 27700023 + Homo 4045 sapiens 1006 chr11 BDNF 27716599 27720680 + Homo 4081 sapiens 1007 chr11 BDNF 27523708 27523784 + Homo 76 sapiens 1008 chr11 BDNF 27527959 27528009 + Homo 50 sapiens 1009 chr11 BDNF 27528063 27528106 + Homo 43 sapiens 1010 chr11 BDNF 27521708 27525784 + Homo 4076 sapiens 1011 chr11 BDNF 27525959 27530009 + Homo 4050 sapiens 1012 chr11 BDNF 27526063 27530106 + Homo 4043 sapiens 1013 chr11 BDNF 27734836 27734884 + Homo 48 sapiens 1014 chr11 BDNF 27740311 27740344 + Homo 33 sapiens 1015 chr11 BDNF 27741786 27741828 + Homo 42 sapiens 1016 chr11 BDNF 27742450 27742493 + Homo 43 sapiens 1017 chr11 BDNF 27732836 27736884 + Homo 4048 sapiens 1018 chr11 BDNF 27738311 27742344 + Homo 4033 sapiens 1019 chr11 BDNF 27739786 27743828 + Homo 4042 sapiens 1020 chr11 BDNF 27740450 27744493 + Homo 4043 sapiens 1021 chr3 ADIPOQ 186548462 186588252 + Homo 39790 sapiens 1022 chr3 ADIPOQ 186548462 186588252 − Homo 39790 sapiens 1023 chr16 Adipoq 23134608 23170041 + Mus 35433 musculus 1024 chr16 Adipoq 23134608 23170041 − Mus 35433 musculus 1025 chr3 ADIPOQ 186566781 186566827 + Homo 46 sapiens 1026 chr3 ADIPOQ 186571630 186571674 + Homo 44 sapiens 1027 chr3 ADIPOQ 186564781 186568827 + Homo 4046 sapiens 1028 chr3 ADIPOQ 186569630 186573674 + Homo 4044 sapiens 1029 chr3 ADIPOQ 186572160 186572189 − Homo 29 sapiens 1030 chr3 ADIPOQ 186570160 186574189 − Homo 4029 sapiens 1031 chrX MECP2 153275263 153375188 − Homo 99925 sapiens 1032 chrX MECP2 153275263 153375188 + Homo 99925 sapiens 1033 chrX Mecp2 71260160 71342932 − Homo 82772 sapiens 1034 chrX Mecp2 71260160 71342932 + Homo 82772 sapiens 1035 chrX MECP2 153278064 153278111 − Homo 47 sapiens 1036 chrX MECP2 153278111 153278156 − Homo 45 sapiens 1037 chrX MECP2 153278706 153278747 − Homo 41 sapiens 1038 chrX MECP2 153279512 153279556 − Homo 44 sapiens 1039 chrX MECP2 153279613 153279658 − Homo 45 sapiens 1040 chrX MECP2 153281486 153281531 − Homo 45 sapiens 1041 chrX MECP2 153283707 153283737 − Homo 30 sapiens 1042 chrX MECP2 153284059 153284105 − Homo 46 sapiens 1043 chrX MECP2 153287944 153287992 − Homo 48 sapiens 1044 chrX MECP2 153288681 153288722 − Homo 41 sapiens 1045 chrX MECP2 153290087 153290134 − Homo 47 sapiens 1046 chrX MECP2 153290216 153290263 − Homo 47 sapiens 1047 chrX MECP2 153290364 153290414 − Homo 50 sapiens 1048 chrX MECP2 153291585 153291633 − Homo 48 sapiens 1049 chrX MECP2 153292312 153292362 − Homo 50 sapiens 1050 chrX MECP2 153292731 153292774 − Homo 43 sapiens 1051 chrX MECP2 153293138 153293185 − Homo 47 sapiens 1052 chrX MECP2 153293331 153293377 − Homo 46 sapiens 1053 chrX MECP2 153293427 153293469 − Homo 42 sapiens 1054 chrX MECP2 153293568 153293614 − Homo 46 sapiens 1055 chrX MECP2 153293715 153293764 − Homo 49 sapiens 1056 chrX MECP2 153293792 153293878 − Homo 86 sapiens 1057 chrX MECP2 153293901 153293948 − Homo 47 sapiens 1058 chrX MECP2 153294420 153294467 − Homo 47 sapiens 1059 chrX MECP2 153297927 153297972 − Homo 45 sapiens 1060 chrX MECP2 153315466 153315571 − Homo 105 sapiens 1061 chrX MECP2 153343401 153343447 − Homo 46 sapiens 1062 chrX MECP2 153344298 153344339 − Homo 41 sapiens 1063 chrX MECP2 153348654 153348702 − Homo 48 sapiens 1064 chrX MECP2 153348997 153349021 − Homo 24 sapiens 1065 chrX MECP2 153349179 153349222 − Homo 43 sapiens 1066 chrX MECP2 153349694 153349734 − Homo 40 sapiens 1067 chrX MECP2 153350493 153350518 − Homo 25 sapiens 1068 chrX MECP2 153356667 153356713 − Homo 46 sapiens 1069 chrX MECP2 153356742 153356795 − Homo 53 sapiens 1070 chrX MECP2 153357047 153357106 − Homo 59 sapiens 1071 chrX MECP2 153357161 153357204 − Homo 43 sapiens 1072 chrX MECP2 153361085 153361163 − Homo 78 sapiens 1073 chrX MECP2 153361423 153361467 − Homo 44 sapiens 1074 chrX MECP2 153362464 153362527 − Homo 63 sapiens 1075 chrX MECP2 153276064 153280111 − Homo 4047 sapiens 1076 chrX MECP2 153276111 153280156 − Homo 4045 sapiens 1077 chrX MECP2 153276706 153280747 − Homo 4041 sapiens 1078 chrX MECP2 153277512 153281556 − Homo 4044 sapiens 1079 chrX MECP2 153277613 153281658 − Homo 4045 sapiens 1080 chrX MECP2 153279486 153283531 − Homo 4045 sapiens 1081 chrX MECP2 153281707 153285737 − Homo 4030 sapiens 1082 chrX MECP2 153282059 153286105 − Homo 4046 sapiens 1083 chrX MECP2 153285944 153289992 − Homo 4048 sapiens 1084 chrX MECP2 153286681 153290722 − Homo 4041 sapiens 1085 chrX MECP2 153288087 153292134 − Homo 4047 sapiens 1086 chrX MECP2 153288216 153292263 − Homo 4047 sapiens 1087 chrX MECP2 153288364 153292414 − Homo 4050 sapiens 1088 chrX MECP2 153289585 153293633 − Homo 4048 sapiens 1089 chrX MECP2 153290312 153294362 − Homo 4050 sapiens 1090 chrX MECP2 153290731 153294774 − Homo 4043 sapiens 1091 chrX MECP2 153291138 153295185 − Homo 4047 sapiens 1092 chrX MECP2 153291331 153295377 − Homo 4046 sapiens 1093 chrX MECP2 153291427 153295469 − Homo 4042 sapiens 1094 chrX MECP2 153291568 153295614 − Homo 4046 sapiens 1095 chrX MECP2 153291715 153295764 − Homo 4049 sapiens 1096 chrX MECP2 153291792 153295878 − Homo 4086 sapiens 1097 chrX MECP2 153291901 153295948 − Homo 4047 sapiens 1098 chrX MECP2 153292420 153296467 − Homo 4047 sapiens 1099 chrX MECP2 153295927 153299972 − Homo 4045 sapiens 1100 chrX MECP2 153313466 153317571 − Homo 4105 sapiens 1101 chrX MECP2 153341401 153345447 − Homo 4046 sapiens 1102 chrX MECP2 153342298 153346339 − Homo 4041 sapiens 1103 chrX MECP2 153346654 153350702 − Homo 4048 sapiens 1104 chrX MECP2 153346997 153351021 − Homo 4024 sapiens 1105 chrX MECP2 153347179 153351222 − Homo 4043 sapiens 1106 chrX MECP2 153347694 153351734 − Homo 4040 sapiens 1107 chrX MECP2 153348493 153352518 − Homo 4025 sapiens 1108 chrX MECP2 153354667 153358713 − Homo 4046 sapiens 1109 chrX MECP2 153354742 153358795 − Homo 4053 sapiens 1110 chrX MECP2 153355047 153359106 − Homo 4059 sapiens 1111 chrX MECP2 153355161 153359204 − Homo 4043 sapiens 1112 chrX MECP2 153359085 153363163 − Homo 4078 sapiens 1113 chrX MECP2 153359423 153363467 − Homo 4044 sapiens 1114 chrX MECP2 153360464 153364527 − Homo 4063 sapiens 1115 chrX MECP2 153279614 153279660 + Homo 46 sapiens 1116 chrX MECP2 153281662 153281720 + Homo 58 sapiens 1117 chrX MECP2 153281946 153281988 + Homo 42 sapiens 1118 chrX MECP2 153284367 153284448 + Homo 81 sapiens 1119 chrX MECP2 153284489 153284534 + Homo 45 sapiens 1120 chrX MECP2 153288786 153288832 + Homo 46 sapiens 1121 chrX MECP2 153289895 153289940 + Homo 45 sapiens 1122 chrX MECP2 153292315 153292365 + Homo 50 sapiens 1123 chrX MECP2 153292496 153292548 + Homo 52 sapiens 1124 chrX MECP2 153297642 153297688 + Homo 46 sapiens 1125 chrX MECP2 153297723 153297765 + Homo 42 sapiens 1126 chrX MECP2 153300816 153300879 + Homo 63 sapiens 1127 chrX MECP2 153315579 153315621 + Homo 42 sapiens 1128 chrX MECP2 153316595 153316640 + Homo 45 sapiens 1129 chrX MECP2 153348783 153348830 + Homo 47 sapiens 1130 chrX MECP2 153349199 153349250 + Homo 51 sapiens 1131 chrX MECP2 153358221 153358285 + Homo 64 sapiens 1132 chrX MECP2 153277614 153281660 + Homo 4046 sapiens 1133 chrX MECP2 153279662 153283720 + Homo 4058 sapiens 1134 chrX MECP2 153279946 153283988 + Homo 4042 sapiens 1135 chrX MECP2 153282367 153286448 + Homo 4081 sapiens 1136 chrX MECP2 153282489 153286534 + Homo 4045 sapiens 1137 chrX MECP2 153286786 153290832 + Homo 4046 sapiens 1138 chrX MECP2 153287895 153291940 + Homo 4045 sapiens 1139 chrX MECP2 153290315 153294365 + Homo 4050 sapiens 1140 chrX MECP2 153290496 153294548 + Homo 4052 sapiens 1141 chrX MECP2 153295642 153299688 + Homo 4046 sapiens 1142 chrX MECP2 153295723 153299765 + Homo 4042 sapiens 1143 chrX MECP2 153298816 153302879 + Homo 4063 sapiens 1144 chrX MECP2 153313579 153317621 + Homo 4042 sapiens 1145 chrX MECP2 153314595 153318640 + Homo 4045 sapiens 1146 chrX MECP2 153346783 153350830 + Homo 4047 sapiens 1147 chrX MECP2 153347199 153351250 + Homo 4051 sapiens 1148 chrX MECP2 153356221 153360285 + Homo 4064 sapiens 1149 chrX FOXP3 49094896 49133288 − Homo 38392 sapiens 1150 chrX FOXP3 49094896 49133288 + Homo 38392 sapiens 1151 chrX Foxp3 7567675 7607243 + Mus 39568 musculus 1152 chrX Foxp3 7567675 7607243 − Mus 39568 musculus 1153 chrX FOXP3 49091852 49146158 + Homo 54306 sapiens 1154 chrX FOXP3 49105387 49126985 + Homo 21598 sapiens 1155 chrX FOXP3 49105442 49121156 + Homo 15714 sapiens 1156 chrX FOXP3 49131266 49131313 + Homo 47 sapiens 1157 chrX FOXP3 49131123 49131172 + Homo 49 sapiens 1158 chrX FOXP3 49127994 49128033 + Homo 39 sapiens 1159 chrX FOXP3 49127843 49127890 + Homo 47 sapiens 1160 chrX FOXP3 49127628 49127670 + Homo 42 sapiens 1161 chrX FOXP3 49124798 49124897 + Homo 99 sapiens 1162 chrX FOXP3 49123918 49123965 + Homo 47 musculus 1163 chrX FOXP3 49120701 49120753 + Homo 52 sapiens 1164 chrX FOXP3 49118531 49118555 + Homo 24 sapiens 1165 chrX FOXP3 49115652 49115685 + Homo 33 sapiens 1166 chrX FOXP3 49112995 49113044 + Homo 49 sapiens 1167 chrX FOXP3 49112863 49112906 + Homo 43 sapiens 1168 chrX FOXP3 49112637 49112717 + Homo 80 sapiens 1169 chrX FOXP3 49107522 49107575 + Homo 53 sapiens 1170 chrX FOXP3 49106607 49106653 + Homo 46 sapiens 1171 chrX FOXP3 49106128 49106175 + Homo 47 sapiens 1172 chrX FOXP3 49105839 49105886 + Homo 47 sapiens 1173 chrX FOXP3 49105669 49105701 + Homo 32 sapiens 1174 chrX FOXP3 49105241 49105285 + Homo 44 sapiens 1175 chrX FOXP3 49089852 49148158 + Homo 58306 sapiens 1176 chrX FOXP3 49103387 49128985 + Homo 25598 sapiens 1177 chrX FOXP3 49103442 49123156 + Homo 19714 sapiens 1178 chrX FOXP3 49129266 49133313 + Homo 4047 sapiens 1179 chrX FOXP3 49129123 49133172 + Homo 4049 sapiens 1180 chrX FOXP3 49125994 49130033 + Homo 4039 sapiens 1181 chrX FOXP3 49125843 49129890 + Homo 4047 sapiens 1182 chrX FOXP3 49125628 49129670 + Homo 4042 sapiens 1183 chrX FOXP3 49122798 49126897 + Homo 4099 sapiens 1184 chrX FOXP3 49121918 49125965 + Homo 4047 sapiens 1185 chrX FOXP3 49118701 49122753 + Homo 4052 sapiens 1186 chrX FOXP3 49116531 49120555 + Homo 4024 sapiens 1187 chrX FOXP3 49113652 49117685 + Homo 4033 sapiens 1188 chrX FOXP3 49110995 49115044 + Homo 4049 sapiens 1189 chrX FOXP3 49110863 49114906 + Homo 4043 sapiens 1190 chrX FOXP3 49110637 49114717 + Homo 4080 sapiens 1191 chrX FOXP3 49105522 49109575 + Homo 4053 sapiens 1192 chrX FOXP3 49104607 49108653 + Homo 4046 sapiens 1193 chrX FOXP3 49104128 49108175 + Homo 4047 sapiens 1194 chrX FOXP3 49103839 49107886 + Homo 4047 sapiens 1195 chrX FOXP3 49103669 49107701 + Homo 4032 sapiens 1196 chrX FOXP3 49103241 49107285 + Homo 4044 sapiens 1197 chrX FOXP3 49091852 49146158 − Homo 54306 sapiens 1198 chrX FOXP3 49105387 49126985 − Homo 21598 sapiens 1199 chrX FOXP3 49127432 49127481 − Homo 49 sapiens 1200 chrX FOXP3 49127343 49127398 − Homo 55 sapiens 1201 chrX FOXP3 49117756 49117794 − Homo 38 sapiens 1202 chrX FOXP3 49100610 49100635 − Homo 25 sapiens 1203 chrX FOXP3 49100129 49100194 − Homo 65 sapiens 1204 chrX FOXP3 49099553 49099595 − Homo 42 sapiens 1205 chrX FOXP3 49089852 49148158 − Homo 58306 sapiens 1206 chrX FOXP3 49103387 49128985 − Homo 25598 sapiens 1207 chrX FOXP3 49125432 49129481 − Homo 4049 sapiens 1208 chrX FOXP3 49125343 49129398 − Homo 4055 sapiens 1209 chrX FOXP3 49115756 49119794 − Homo 4038 sapiens 1210 chrX FOXP3 49098610 49102635 − Homo 4025 sapiens 1211 chrX FOXP3 49098129 49102194 − Homo 4065 sapiens 1212 chrX FOXP3 49097553 49101595 − Homo 4042 sapiens

Table 2: Imprinted Regions Hit by the Expanded PRC2 Transcriptome.

Intersection of the PRC2 transcriptome with imprinted gene coordinates (available online at geneimprint.com). The murine imprinted gene (i.e., an intersecting or nearby gene) targeted by the PRC2 binding transcript is shown in column 1. Column 1 also shows the chromosome strand of the murine imprinted gene (“+” sign indicates that the gene is transcribed from the top or plus strand, while “−” sign indicates that the PRC2 binding transcript is transcribed from the bottom or minus strand of the chromosome). The chromosome localization and nucleotide coordinates in mm9 of the PRC2 binding transcript are shown in column 2, as well as a “+” sign or “−” sign that indicates whether the PRC2 binding transcript is transcribed from the top strand (plus strand hit) or bottom strand (minus strand hit) of the chromosome. Column 3 displays the sequence identifiers of the mouse PRC2 binding transcript (i.e., the nucleotide sequence transcribed from the mouse chromosomal coordinates and strand of column 2, converted to RNA by replacing T with U). Column 4 shows the corresponding human gene name for the murine imprinted gene of column 1, obtained from the Mouse Genome Database (MGD), Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Me. World Wide Web (informatics.jax.org). Mouse to human LiftOver of the mouse chromosome coordinates in column 2, performed in the UCSC genome browser as described herein, generated the orthologous human chromosome coordinates which appear in Column 5. 50% conservation was used for LiftOver analysis. Additional human chromosome coordinates were generated by mapping of highly conserved or homologous regions from the mouse to human genome. Column 6 displays the sequence identifiers of the predicted human PRC2 binding transcript (i.e., the nucleotide sequence transcribed from the human chromosomal coordinates and strand of column 5, converted to RNA by replacing T with U). When the PRC2 interacting transcript is transcribed from the opposite strand compared to the imprinted reference gene in column 1, that implies that the PRC2 interacting RNA is complementary, or antisense strand (“opposite strand”) in orientation, to the reference imprinted gene. Note that the PRC2 binding transcript need not be the reference imprinted gene itself, but a distinct transcript that overlaps in position.

Table 3: Hexamers that are not Seed Sequences of Human miRNAs

APPENDIX I, of U.S. provisional application 61/425,174 filed on Dec. 20, 2010, the entirety of which is incorporated by reference herein, is a listing of a complete RIP seq dataset, showing all of the reads in the dataset. Appendix I is not attached hereto. The sequence reads in Appendix I come directly off the Illumina GA II genome analyzer and are in an orientation that is the reverse complement of the PRC2 binding transcript. Appendix I is a filtered subset of all of the reads after bioinformatic filtering removed adaptor/primer dimers, mitochondrial RNA, rRNA, homopolymers, reads with indeterminate nucleotides, and truncated reads (<15nt).

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION

Aspects of the invention provided herein relate to the discovery of polycomb repressive complex 2 (PRC2)-interacting RNAs. Polycomb repressive complex 2 (PRC2) is a histone methyltransferase and a known epigenetic regulator involved in silencing of genomic regions through methylation of histone H3. Among other functions, PRC2 interacts with long noncoding RNAs (lncRNAs), such as RepA and Xist, and Tsix, to catalyze trimethylation of histone H3-lysine27. PRC2 contains four subunits, Eed, Suz12, RbAp48, and Ezh2.

A method, referred to herein as “RNA immunoprecipitation (RIP)-seq,” was used to identify a genome-wide pool of >100,000 polycomb repressive complex 2 (PRC2)-interacting RNAs in embryonic stem cells. A large number of transcripts occur within and around imprinted regions, oncogene and tumor suppressor loci, and stem-cell-related bivalent domains. Evidence for direct RNA-protein interactions, some via the Ezh2 subunit, was established. Further evidence was established that single stranded oligonucleotides designed to bind to these PRC2-interacting RNAs can successfully up-regulate gene expression in a variety of separate and independent examples, which is believed to result from inhibition of PRC2 mediated repression of these target genes. Thus, PRC2 complexes interact with a genome-wide family of RNAs, which may be used as therapeutic targets for human disease. In some embodiments, the sequences of RNA's that interact with PRC2 were between 40-60 nucleotides in length.

As used herein, the term “PRC2-associated region” refers to a region of a nucleic acid that comprises or encodes a sequence of nucleotides that interact directly or indirectly with a component of PRC2. A PRC2-associated region may be present in a RNA (e.g., a long non-coding RNA (lncRNA)) that that interacts with a PRC2. A PRC2-associated region may be present in a DNA that encodes an RNA that interacts with a PRC2.

In some embodiments, a PRC2-associated region is a region of an RNA that crosslinks to a component of PRC2 in response to in situ ultraviolet irradiation of a cell that expresses the RNA, or a region of genomic DNA that encodes that RNA region. In some embodiments, a PRC2-associated region is a region of an RNA that immunoprecipitates with an antibody that targets a component of PRC2, or a region of genomic DNA that encodes that RNA region. In some embodiments, a PRC2-associated region is a region of an RNA that immunoprecipitates with an antibody that targets SUZ12, EED, EZH2 or RBBP4 (which are components of PRC2), or a region of genomic DNA that encodes that RNA region.

In some embodiments, a PRC2-associated region is a region of an RNA that is protected from nucleases (e.g., RNases) in an RNA-immunoprecipitation assay that employs an antibody that targets a component of PRC2, or a region of genomic DNA that encodes that protected RNA region. In some embodiments, a PRC2-associated region is a region of an RNA that is protected from nucleases (e.g., RNases) in an RNA-immunoprecipitation assay that employs an antibody that targets SUZ12, EED, EZH2 or RBBP4, or a region of genomic DNA that encodes that protected RNA region.

In some embodiments, a PRC2-associated region is a region of an RNA within which occur a relatively high frequency of sequence reads in a sequencing reaction of products of an RNA-immunoprecipitation assay that employs an antibody that targets a component of PRC2, or a region of genomic DNA that encodes that RNA region. In some embodiments, a PRC2-associated region is a region of an RNA within which occur a relatively high frequency of sequence reads in a sequencing reaction of products of an RNA-immunoprecipitation assay that employs an antibody that targets SUZ12, EED, EZH2 or RBBP4, or a region of genomic DNA that encodes that protected RNA region. In such embodiments, the PRC2-associated region may be referred to as a “peak.”

In some embodiments, a PRC2-associated region comprises a sequence of 40 to 60 nucleotides that interact with PRC2 complex. In some embodiments, a PRC2-associated region comprises a sequence of 40 to 60 nucleotides that encode an RNA that interacts with PRC2. In some embodiments, a PRC2-associated region comprises a sequence of up to 5 kb in length that comprises a sequence (e.g., of 40 to 60 nucleotides) that interacts with PRC2. In some embodiments, a PRC2-associated region comprises a sequence of up to 5 kb in length within which an RNA is encoded that has a sequence (e.g., of 40 to 60 nucleotides) that is known to interact with PRC2. In some embodiments, a PRC2-associated region comprises a sequence of about 4 kb in length that comprise a sequence (e.g., of 40 to 60 nucleotides) that interacts with PRC2. In some embodiments, a PRC2-associated region comprises a sequence of about 4 kb in length within which an RNA is encoded that includes a sequence (e.g., of 40 to 60 nucleotides) that is known to interact with PRC2.

In some embodiments, a PRC2-associated region has a sequence as set forth in any one of sequences A1 to A193,049, B1 to B916,209, and B916,626 to B934,931.

In some embodiments, single stranded oligonucleotides are provided that specifically bind to, or are complementary to, a PRC2-associated region, for example, a nucleic acid having a sequence as set forth in sequences A1 to A193,049, B1 to B916,209, and B916,626 to B934,931. Without being bound by a theory of invention, these oligonucleotides are able to interfere with the binding of and function of PRC2, by preventing recruitment of PRC2 to a specific chromosomal locus. For example, data herein shows that a single administration of single stranded oligonucleotides designed to specifically bind a PRC2-associated region lncRNA can stably displace not only the lncRNA, but also the PRC2 that binds to the lncRNA, from binding chromatin. After displacement, the full complement of PRC2 is not recovered for up to 24 hours. Further, data provided herein support that lncRNA can recruit PRC2 in a cis fashion, repressing gene expression at or near the specific chromosomal locus from which the lncRNA was transcribed, thus making it possible to design oligonucleotides that inhibit the function of PRC2 and increase the expression of a specific target gene.

In further aspects of the invention, methods are provided for selecting a candidate oligonucleotide for activating expression of a target gene. The methods generally involve selecting as a candidate oligonucleotide, a single stranded oligonucleotide comprising a nucleotide sequence that is complementary to a PRC2-associated region (e.g., a nucleotide sequence as set forth in sequences A1 to A193,049, B1 to B916,209, and B916,626 to B934,931). In some embodiments, sets of oligonucleotides may be selected that are enriched (e.g., compared with a random selection of oligonucleotides) in oligonucleotides that activate expression of a target gene.

In some embodiments, the single stranded oligonucleotide is provided for use in a method of modulating expression of a “gene targeted by the PRC2-binding RNA” (e.g., an intersecting or nearby gene, as set forth in Tables 1-3), meaning a gene whose expression is regulated by the PRC2-binding RNA. The term “PRC2-binding RNA” or “RNA that binds PRC2” is used interchangeably with “PRC2-associated RNA” and “PRC2-interacting RNA”, and refers to a lncRNA, RNA transcript or a PRC2-associated region thereof (e.g., a Peak as described below) that binds PRC2, directly or indirectly. Such binding may be determined by immunoprecipitation techniques using antibodies to a component of the PRC2 complex, e.g. Ezh2. Sequences A1 to A193,049, B1 to B916,209, and B916,626 to B934,931 represent murine RNA sequences containing portions that have been experimentally determined to bind PRC2 using the RIP-seq method described herein, or human RNA sequences corresponding to these murine RNA sequences.

Such methods of modulating gene expression may be carried out in vitro, ex vivo, or in vivo. Table 8 of International Patent Application Publication WO/2012/065143 displays genes targeted by the PRC2-binding RNA; the sequence identifiers of the PRC2-binding

RNA are set forth in the same row as the gene name. In some embodiments, a single stranded oligonucleotide is provided for use in a method of treating disease, e.g. a disease category as set forth in Table 9 of International Patent Application Publication WO/2012/065143 or Table 2. Table 2 of International Patent Application Publication WO/2012/087983, displays genes targeted by the PRC2-binding RNA; the sequence identifiers of the PRC2-binding RNA are set forth in the same row as the gene name. In some embodiments, a single stranded oligonucleotide is provided for use in a method of treating disease, e.g. a disease category as set forth in Table 3 of International Patent Application Publication WO/2012/087983 or Table 2. The treatment may involve modulating expression of a gene targeted by the PRC2-binding RNA, preferably upregulating gene expression. The single stranded oligonucleotide may be formulated as a sterile composition for parenteral administration. It is understood that any reference to uses of compounds throughout the description contemplates use of the compound in preparation of a pharmaceutical composition or medicament for use in the treatment of a disease. Thus, as one nonlimiting example, this aspect of the invention includes use of such single stranded oligonucleotides in the preparation of a medicament for use in the treatment of disease, wherein the treatment involves upregulating expression of a gene targeted by the PRC2-binding RNA.

Method for Selecting Candidate Oligonucleotides for Activating Gene Expression

Methods are provided herein for selecting a candidate oligonucleotide for activating expression of a target gene. The target gene of interest may, for example, be a gene of Table 9 of International Patent Application Publication WO/2012/065143. The target gene of interest may, for example, be a gene of Table 3 of International Patent Application Publication WO/2012/087983. The target gene of interest may be FXN, SMN1, SMN2, SMNP, UTRN, HBB, HBD, HBE1, HBG1, HBG2, Hbb-b1, Hbb-bh1, Hbb-y, HBB/HBD, ATP2A2, APOA1, Abca1, PTEN, BDNF, BDNF-AS1, ADIPOQ, MECP2 or FOXP3. Accordingly, the candidate oligonucleotide may be complementary to a sequence selected from the sequences set forth in SEQ ID NOS: 1-1212.

Typically, the methods involve one or more steps aimed at identifying oligonucleotides that target a PRC2-associated region that is functionally related to the target gene, for example a PRC2-associated region of a lncRNA that regulates expression of the target gene by facilitating (e.g., in a cis-regulatory manner) the recruitment of PRC2 to the target gene. Such oligonucleotides are expected to be candidates for activating expression of the target gene because of their ability to hybridize with the PRC2-associated region of a nucleic acid (e.g., a lncRNA). In some embodiments, this hybridization event is understood to disrupt interaction of PRC2 with the nucleic acid (e.g., a lncRNA) and as a result disrupt recruitment of PRC2 and its associated co-repressors (e.g., chromatin remodeling factors) to the target gene locus.

Methods of selecting a candidate oligonucleotide may involve selecting a PRC2-associated region (e.g., a nucleotide sequence as set forth in sequences A1 to A193,049, B1 to B916,209, and B916,626 to B934,931) that maps to a chromosomal position encompassing or in proximity to a target gene of interest. The PRC2-associated region may map to the strand of the chromosome comprising the sense strand of the target gene, in which case the candidate oligonucleotide is complementary to the sense strand of the target gene (i.e., is antisense to the target gene). Alternatively, the PRC2-associated region may map to the strand of the first chromosome comprising the antisense strand of the target gene, in which case the oligonucleotide is complementary to the antisense strand (the template strand) of the target gene (i.e., is sense to the target gene).

Methods for selecting a set of candidate oligonucleotides that is enriched in oligonucleotides that activate expression of a target gene may involve selecting one or more PRC2-associated regions that maps to a chromosomal position that encompasses or that is in proximity to the target gene and selecting a set of oligonucleotides, in which each oligonucleotide in the set comprises a nucleotide sequence that is complementary with the one or more PRC2-associated regions. As used herein, the phrase, “a set of oligonucleotides that is enriched in oligonucleotides that activate expression of a target gene” refers to a set of oligonucleotides that has a greater number of oligonucleotides that activate expression of a target gene compared with a random selection of oligonucleotides of the same physicochemical properties (e.g., the same GC content, T_(m), length etc.) as the enriched set.

The PRC2-associated region may map to a position in a chromosome between 50 kilobases upstream of a 5′-end of the target gene and 50 kilobases downstream of a 3′-end of the target gene. The PRC2-associated region may map to a position in a chromosome between 25 kilobases upstream of a 5′-end of the target gene and 25 kilobases downstream of a 3′-end of the target gene. The PRC2-associated region may map to a position in a chromosome between 12 kilobases upstream of a 5′-end of the target gene and 12 kilobases downstream of a 3′-end of the target gene. The PRC2-associated region may map to a position in a chromosome between 5 kilobases upstream of a 5′-end of the target gene and 5 kilobases downstream of a 3′-end of the target gene.

The genomic position of the selected PRC2-associated region relative to the target gene may vary. For example, the PRC2-associated region may be upstream of the 5′ end of the target gene. The PRC2-associated region may be downstream of the 3′ end of the target gene. The PRC2-associated region may be within an intron of the target gene. The PRC2-associated region may be within an exon of the target gene. The PRC2-associated region may traverse an intron-exon junction, a 5′-UTR-exon junction or a 3′-UTR-exon junction of the target gene.

The candidate oligonucleotide selection methods may generally also involve determining or identifying an appropriate nucleotide sequence that is complementary with the PRC2-associated region. This nucleotide sequence may be complementary with at least 6, at least 7, at least 8, at least 9, at least 10, at least 15 or more consecutive nucleotides of the PRC2-associated region.

The candidate oligonucleotide may comprise a sequence having the formula X-Y-Z, in which X is any nucleotide, Y is a nucleotide sequence of 6 nucleotides in length that is not a human seed sequence of a microRNA, and Z is a nucleotide sequence of varying length. In some embodiments X is anchored at the 5′ end of the oligonucleotide. In some embodiments, when X is anchored at the 5′ end of the oligonucleotide, the oligonucleotide does not have any nucleotides or nucleotide analogs linked 5′ to X. In some embodiments, other compounds such as peptides or sterols may be linked at the 5′ end in this embodiment as long as they are not nucleotides or nucleotide analogs. Candidate oligonucleotides that have these sequence characteristics are predicted to avoid the miRNA pathway. Therefore, in some embodiments, oligonucleotides having these sequence characteristics unlikely to have an unintended consequence of functioning in a cell as a miRNA molecule. The Y sequence may be a nucleotide sequence of 6 nucleotides in length set forth in Table 3.

The candidate oligonucleotide may have a sequence that does not contain guanosine nucleotide stretches (e.g., 3 or more, 4 or more, 5 or more, 6 or more consecutive guanosine nucleotides). In some embodiments, oligonucleotides having guanosine nucleotide stretches have increased non-specific binding and/or off-target effects, compared with oligonucleotides that do not have guanosine nucleotide stretches.

The candidate oligonucleotide may be selected such that it has a sequence that has less than a threshold level of sequence identity with every sequence of nucleotides, of equivalent length, that map to a genomic position encompassing or in proximity to an off-target gene. For example, a candidate oligonucleotide may be designed to ensure that it does not have a sequence that maps to genomic positions encompassing or in proximity with all known genes (e.g., all known protein coding genes) other than the target gene. In a similar embodiment, a candidate oligonucleotide may be designed to ensure that it does not have a sequence that maps to any other known PRC2-associated region (e.g., a nucleotide sequence as set forth in sequences A1 to A193,049, B1 to B916,209, and B916,626 to B934,931), particularly PRC2-associated regions that are functionally related to any other known gene (e.g., any other known protein coding gene). In either case, the candidate oligonucleotide is expected to have a reduced likelihood of having off-target effects. The threshold level of sequence identity may be 50%, 60%, 70%, 80%, 85%, 90%, 95% or 99% sequence identity.

The candidate oligonucleotide may be selected such that it has a sequence that is complementary to a PRC2-associated region that encodes an RNA that forms a secondary structure comprising at least two single stranded loops. In has been discovered that, in some embodiments, oligonucleotides that are complementary to a PRC2-associated region that encodes an RNA that forms a secondary structure comprising one or more single stranded loops (e.g., at least two single stranded loops) have a greater likelihood of being active than a randomly selected oligonucleotide. In some cases, the secondary structure may comprise a double stranded stem between the at least two single stranded loops. Accordingly, the selection methods may involve selecting a sequence for the oligonucleotide such that the region of complementarity between the oligonucleotide and the PRC2-associated region is at a location of the PRC2 associated region that encodes at least a portion of at least one of the loops. In some cases, the selection methods may involve selecting a sequence for the oligonucleotide such that the region of complementarity between the oligonucleotide and the PRC2-associated region is at a location of the PRC2-associated region that encodes at least a portion of at least two of the loops. In some cases, the selection methods may involve selecting a sequence for the oligonucleotide such that the region of complementarity between the oligonucleotide and the PRC2-associated region is at a location of the PRC2 associated region that encodes at least a portion of the double stranded stem. In some embodiments, a PRC2-associated region (e.g., of an lncRNA) is identified (e.g., using RIP-Seq methodology or information derived therefrom). In some embodiments, the predicted secondary structure RNA (e.g., lncRNA) containing the PRC2-associated region is determined using RNA secondary structure prediction algorithms, e.g., RNAfold, mfold. In some embodiments, oligonucleotides are designed to target a region of the RNA that forms a secondary structure comprising one or more single stranded loop (e.g., at least two single stranded loops) structures which may comprise a double stranded stem between the at least two single stranded loops.

The candidate oligonucleotide may be selected such that it has a sequence that is has greater than 30% G-C content, greater than 40% G-C content, greater than 50% G-C content, greater than 60% G-C content, greater than 70% G-C content, or greater than 80% G-C content. In some embodiments in which the oligonucleotide is 8 to 10 nucleotides in length, all but 1, 2, 3, 4, or 5 of the nucleotides of the complementary sequence of the PRC2-associated region are cytosine or guanosine nucleotides.

The candidate oligonucleotide selection methods may also involve determining that the candidate oligonucleotide is complementary to a chromosome of a different species (e.g., a mouse, rat, rabbit, goat, monkey, etc.) at a position that encompasses or that is in proximity to the homolog of the target gene. This enables the design of oligonucleotides that may be tested in vivo or in vitro for efficacy in multiple species (e.g., human and mouse). This approach also facilitates development of clinical candidates for treating human disease by selecting a species in which an appropriate animal exists for the disease. The candidate oligonucleotide can be readily tested in the animal model.

Where the design and/or synthesis of a single stranded oligonucleotide involves design and/or synthesis of a sequence that is complementary to a nucleic acid or PRC2-associated region described by such sequence information, the skilled person is readily able to determine the complementary sequence, e.g., through understanding of Watson Crick base pairing rules which form part of the common general knowledge in the field.

In some embodiments design and/or synthesis of a single stranded oligonucleotide involves manufacture of an oligonucleotide from starting materials by techniques known to those of skill in the art, where the synthesis may be based on a sequence of a PRC2-associated region, or portion thereof.

Methods of design and/or synthesis of a single stranded oligonucleotide may involve one or more of the steps of:

Identifying and/or selecting PRC2-associated region;

Designing a nucleic acid sequence having a desired degree of sequence identity or complementarity to a PRC2-associated region or a portion thereof;

Synthesizing a single stranded oligonucleotide to the designed sequence;

Purifying the synthesized single stranded oligonucleotide; and

Optionally mixing the synthesized single stranded oligonucleotide with at least one pharmaceutically acceptable diluent, carrier or excipient to form a pharmaceutical composition or medicament.

Single stranded oligonucleotides so designed and/or synthesized may be useful in method of modulating gene expression as described herein.

Preferably, single stranded oligonucleotides of the invention are synthesized chemically. Oligonucleotides used to practice this invention can be synthesized in vitro by well-known chemical synthesis techniques.

Oligonucleotides of the invention can be stabilized against nucleolytic degradation such as by the incorporation of a modification, e.g., a nucleotide modification. For example, nucleic acid sequences of the invention include a phosphorothioate at least the first, second, or third internucleotide linkage at the 5′ or 3′ end of the nucleotide sequence. As another example, the nucleic acid sequence can include a 2′-modified nucleotide, e.g., a 2′-deoxy, 2′-deoxy-2′-fluoro, 2′-O-methyl, 2′-O-methoxyethyl (2′-O-MOE), 2′-O-aminopropyl (2′-O-AP), 2′-O-dimethylaminoethyl (2′-O-DMAOE), 2′-O-dimethylaminopropyl (2′-O-DMAP), 2′-O-dimethylaminoethyloxyethyl (2′-O-DMAEOE), or 2′-O—N-methylacetamido (2′-O-NMA). As another example, the nucleic acid sequence can include at least one 2′-O-methyl-modified nucleotide, and in some embodiments, all of the nucleotides include a 2′-O-methyl modification. In some embodiments, the nucleic acids are “locked,” i.e., comprise nucleic acid analogues in which the ribose ring is “locked” by a methylene bridge connecting the 2′-O atom and the 4′-C atom.

It is understood that any of the modified chemistries or formats of single stranded oligonucleotides described herein can be combined with each other, and that one, two, three, four, five, or more different types of modifications can be included within the same molecule.

In some embodiments, the method may further comprise the steps of amplifying the synthesized single stranded oligonucleotide, and/or purifying the single stranded oligonucleotide (or amplified single stranded oligonucleotide), and/or sequencing the single stranded oligonucleotide so obtained.

As such, the process of preparing a single stranded oligonucleotide may be a process that is for use in the manufacture of a pharmaceutical composition or medicament for use in the treatment of disease, optionally wherein the treatment involves modulating expression of a gene associated with a PRC2-associated region.

In the methods described above a PRC2-associated region may be, or have been, identified, or obtained, by a method that involves identifying RNA that binds to PRC2.

Such methods may involve the following steps: providing a sample containing nuclear ribonucleic acids, contacting the sample with an agent that binds specifically to PRC2 or a subunit thereof, allowing complexes to form between the agent and protein in the sample, partitioning the complexes, synthesizing nucleic acid that is complementary to nucleic acid present in the complexes.

Where the single stranded oligonucleotide is based on a PRC2-associated region, or a portion of such a sequence, it may be based on information about that sequence, e.g., sequence information available in written or electronic form, which may include sequence information contained in publicly available scientific publications or sequence databases.

Single Stranded Oligonucleotides

In one aspect of the invention, single stranded oligonucleotides complementary to the PRC2-associated regions are provided for modulating expression of target genes in a cell. In some embodiments, expression of target genes is upregulated or increased. In some embodiments, single stranded oligonucleotides complementary to these PRC2-associated regions inhibit the interaction of PRC2 with long RNA transcripts, resulting in reduced methylation of histone H3 and reduced gene inactivation, such that gene expression is upregulated or increased. In some embodiments, this interaction may be disrupted or inhibited due to a change in the structure of the long RNA that prevents or reduces binding to PRC2. The oligonucleotide may be selected using any of the methods disclosed herein for selecting a candidate oligonucleotide for activating expression of a target gene.

In some embodiments, the region of complementarity is complementary with at least 8 to 15, 8 to 30, 8 to 40, or 10 to 50, or 5 to 50, or 5 to 40 bases, e.g., 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 consecutive nucleotides of a PRC2-associated region. In some embodiments, the region of complementarity is complementary with at least 8 consecutive nucleotides of a PRC2-associated region. In some embodiments the sequence of the single stranded oligonucleotide is based on an RNA sequence that binds to PRC2, or a portion thereof, said portion having a length of from 5 to 40 contiguous base pairs, or about 8 to 40 bases, or about 5 to 15, or about 5 to 30, or about 5 to 40 bases, or about 5 to 50 bases.

Any of the oligonucleotides disclosed herein may be linked to one or more other oligonucleotides disclosed herein by a cleavable linker.

Complementary, as the term is used in the art, refers to the capacity for precise pairing between two nucleotides. For example, if a nucleotide at a certain position of an oligonucleotide is capable of hydrogen bonding with a nucleotide at the same position of PRC2-associated region, then the single stranded nucleotide and PRC2-associated region are considered to be complementary to each other at that position. The single stranded nucleotide and PRC2-associated region are complementary to each other when a sufficient number of corresponding positions in each molecule are occupied by nucleotides that can hydrogen bond with each other through their bases. Thus, “complementary” is a term which is used to indicate a sufficient degree of complementarity or precise pairing such that stable and specific binding occurs between the single stranded nucleotide and PRC2-associated region. For example, if a base at one position of a single stranded nucleotide is capable of hydrogen bonding with a base at the corresponding position of a PRC2-associated region, then the bases are considered to be complementary to each other at that position. 100% complementarity is not required.

The single stranded oligonucleotide may be at least 80% complementary to (optionally one of at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% complementary to) the consecutive nucleotides of a PRC2-associated region. In some embodiments the single stranded oligonucleotide may contain 1, 2 or 3 base mismatches compared to the portion of the consecutive nucleotides of a PRC2-associated region. In some embodiments the single stranded oligonucleotide may have up to 3 mismatches over 15 bases, or up to 2 mismatches over 10 bases.

It is understood in the art that a complementary nucleotide sequence need not be 100% complementary to that of its target to be specifically hybridizable. In some embodiments, a complementary nucleic acid sequence for purposes of the present methods is specifically hybridizable when binding of the sequence to the target molecule (e.g., lncRNA) interferes with the normal function of the target (e.g., lncRNA) to cause a loss of activity (e.g., inhibiting PRC2-associated repression with consequent up-regulation of gene expression) and there is a sufficient degree of complementarity to avoid non-specific binding of the sequence to non-target sequences under conditions in which avoidance of non-specific binding is desired, e.g., under physiological conditions in the case of in vivo assays or therapeutic treatment, and in the case of in vitro assays, under conditions in which the assays are performed under suitable conditions of stringency.

In some embodiments, the single stranded oligonucleotide is 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50 or more nucleotides in length. In an embodiment, the oligonucleotide is 8 to 30 nucleotides in length.

In some embodiments, the PRC2-associated region occurs on the same DNA strand as a gene sequence (sense). In some embodiments, the PRC2-associated region occurs on the opposite DNA strand as a gene sequence (anti-sense). Oligonucleotides complementary to a PRC2-associated region can bind either sense or anti-sense sequences. Base pairings may include both canonical Watson-Crick base pairing and non-Watson-Crick base pairing (e.g., Wobble base pairing and Hoogsteen base pairing). It is understood that for complementary base pairings, adenosine-type bases (A) are complementary to thymidine-type bases (T) or uracil-type bases (U), that cytosine-type bases (C) are complementary to guanosine-type bases (G), and that universal bases such as 3-nitropyrrole or 5-nitroindole can hybridize to and are considered complementary to any A, C, U, or T. Inosine (I) has also been considered in the art to be a universal base and is considered complementary to any A, C, U or T.

In some embodiments, any one or more thymidine (T) nucleotides (or modified nucleotide thereof) or uridines (U) nucleotides (or a modified nucleotide thereof) in a sequence provided herein, including a sequence provided in the sequence listing, may be replaced with any other nucleotide suitable for base pairing (e.g., via a Watson-Crick base pair) with an adenosine nucleotide. In some embodiments, any one or more thymidine (T) nucleotides (or modified nucleotide thereof) or uridines (U) nucleotides (or a modified nucleotide thereof) in a sequence provided herein, including a sequence provided in the sequence listing, may be suitably replaced with a different pyrimidine nucleotide or vice versa. In some embodiments, any one or more thymidine (T) nucleotides (or modified nucleotide thereof) in a sequence provided herein, including a sequence provided in the sequence listing, may be suitably replaced with a uridine (U) nucleotide (or a modified nucleotide thereof) or vice versa. Inosine (I) has also been considered in the art to be a universal base and is considered complementary to any A, C, U or T.

Inosine (I) has also been considered in the art to be a universal base and is considered complementary to any A, C, U or T.

In some embodiments, GC content of the single stranded oligonucleotide may be between about 30-60%. Contiguous runs of three or more Gs or Cs may not be preferable in some embodiments. Accordingly, in some embodiments, the oligonucleotide does not comprise a stretch of three or more guanosine nucleotides.

In some embodiments, the single stranded oligonucleotide specifically binds to, or is complementary to an RNA that is encoded in a genome (e.g., a human genome) as a single contiguous transcript (e.g., a non-spliced RNA). In some embodiments, the single stranded oligonucleotide specifically binds to, or is complementary to an RNA that is encoded in a genome (e.g., a human genome), in which the distance in the genome between the 5′end of the coding region of the RNA and the 3′ end of the coding region of the RNA is less than 1 kb, less than 2 kb, less than 3 kb, less than 4 kb, less than 5 kb, less than 7 kb, less than 8 kb, less than 9 kb, less than 10 kb, or less than 20 kb.

It is to be understood that any oligonucleotide provided herein can be excluded. In some embodiments, a single stranded oligonucleotide is not complementary to any one or more of SEQ ID NOs: 1213 to 1226.

Nucleotide Analogues

In some embodiments, the oligonucleotide may comprise at least one ribonucleotide, at least one deoxyribonucleotide, and/or at least one bridged nucleotide. In some embodiments, the oligonucleotide may comprise a bridged nucleotide, such as a LNA nucleotide, a cEt nucleotide or a ENA nucleotide analogue. Examples of such nucleotides are disclosed herein and known in the art. In some embodiments, the oligonucleotide comprises a nucleotide analog disclosed in one of the following United States patent or Patent Application Publications: U.S. Pat. No. 7,399,845, U.S. Pat. No. 7,741,457, U.S. Pat. No. 8,022,193, U.S. Pat. No. 7,569,686, U.S. Pat. No. 7,335,765, U.S. Pat. No. 7,314,923, U.S. Pat. No. 7,335,765, and U.S. Pat. No. 7,816,333, US 20110009471, the entire contents of each of which are incorporated herein by reference for all purposes. The oligonucleotide may have one or more 2′ O-methyl nucleotides. The oligonucleotide may consist entirely of 2′ O-methyl nucleotides.

Often the single stranded oligonucleotide has one or more nucleotide analogues. For example, the single stranded oligonucleotide may have at least one nucleotide analogue that results in an increase in T_(m) of the oligonucleotide in a range of 1° C., 2° C., 3° C., 4° C., or 5° C. compared with an oligonucleotide that does not have the at least one nucleotide analogue.

The single stranded oligonucleotide may have a plurality of nucleotide analogues that results in a total increase in T_(m) of the oligonucleotide in a range of 2° C., 3° C., 4° C., 5° C., 6° C., 7° C., 8° C., 9° C., 10° C., 15° C., 20° C., 25° C., 30° C., 35° C., 40° C., 45° C. or more compared with an oligonucleotide that does not have the nucleotide analogue.

The oligonucleotide may be of up to 50 nucleotides in length in which 2 to 10, 2 to 15, 2 to 16, 2 to 17, 2 to 18, 2 to 19, 2 to 20, 2 to 25, 2 to 30, 2 to 40, 2 to 45, or more nucleotides of the oligonucleotide are nucleotide analogues. The oligonucleotide may be of 8 to 30 nucleotides in length in which 2 to 10, 2 to 15, 2 to 16, 2 to 17, 2 to 18, 2 to 19, 2 to 20, 2 to 25, 2 to 30 nucleotides of the oligonucleotide are nucleotide analogues.

The oligonucleotide may be of 8 to 15 nucleotides in length in which 2 to 4, 2 to 5, 2 to 6, 2 to 7, 2 to 8, 2 to 9, 2 to 10, 2 to 11, 2 to 12, 2 to 13, 2 to 14 nucleotides of the oligonucleotide are nucleotide analogues. Optionally, the oligonucleotides may have every nucleotide except 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides modified.

The oligonucleotide may consist entirely of bridged nucleotides (e.g., LNA nucleotides, cEt nucleotides, ENA nucleotides). The oligonucleotide may comprise alternating deoxyribonucleotides and 2′-fluoro-deoxyribonucleotides. The oligonucleotide may comprise alternating deoxyribonucleotides and 2′-O-methyl nucleotides. The oligonucleotide may comprise alternating deoxyribonucleotides and ENA nucleotide analogues. The oligonucleotide may comprise alternating deoxyribonucleotides and LNA nucleotides. The oligonucleotide may comprise alternating LNA nucleotides and 2′-O-methyl nucleotides. The oligonucleotide may have a 5′ nucleotide that is a bridged nucleotide (e.g., a LNA nucleotide, cEt nucleotide, ENA nucleotide). The oligonucleotide may have a 5′ nucleotide that is a deoxyribonucleotide.

The oligonucleotide may comprise deoxyribonucleotides flanked by at least one bridged nucleotide (e.g., a LNA nucleotide, cEt nucleotide, ENA nucleotide) on each of the 5′ and 3′ ends of the deoxyribonucleotides. The oligonucleotide may comprise deoxyribonucleotides flanked by 1, 2, 3, 4, 5, 6, 7, 8 or more bridged nucleotides (e.g., LNA nucleotides, cEt nucleotides, ENA nucleotides) on each of the 5′ and 3′ ends of the deoxyribonucleotides. The 3′ position of the oligonucleotide may have a 3′ hydroxyl group. The 3′ position of the oligonucleotide may have a 3′ thiophosphate.

The oligonucleotide may be conjugated with a label. For example, the oligonucleotide may be conjugated with a biotin moiety, cholesterol, Vitamin A, folate, sigma receptor ligands, aptamers, peptides, such as CPP, hydrophobic molecules, such as lipids, ASGPR or dynamic polyconjugates and variants thereof at its 5′ or 3′ end.

Preferably the single stranded oligonucleotide comprises one or more modifications comprising: a modified sugar moiety, and/or a modified internucleoside linkage, and/or a modified nucleotide and/or combinations thereof. It is not necessary for all positions in a given oligonucleotide to be uniformly modified, and in fact more than one of the modifications described herein may be incorporated in a single oligonucleotide or even at within a single nucleoside within an oligonucleotide.

In some embodiments, the single stranded oligonucleotides are chimeric oligonucleotides that contain two or more chemically distinct regions, each made up of at least one nucleotide. These oligonucleotides typically contain at least one region of modified nucleotides that confers one or more beneficial properties (such as, for example, increased nuclease resistance, increased uptake into cells, increased binding affinity for the target) and a region that is a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. Chimeric single stranded oligonucleotides of the invention may be formed as composite structures of two or more oligonucleotides, modified oligonucleotides, oligonucleosides and/or oligonucleotide mimetics as described above. Such compounds have also been referred to in the art as hybrids or gapmers. Representative United States patents that teach the preparation of such hybrid structures comprise, but are not limited to, U.S. Pat. Nos. 5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878; 5,403,711; 5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; and 5,700,922, each of which is herein incorporated by reference.

In some embodiments, the single stranded oligonucleotide comprises at least one nucleotide modified at the 2′ position of the sugar, e.g., a 2′-O-alkyl, 2′-O-alkyl-O-alkyl or 2′-fluoro-modified nucleotide. In other embodiments, RNA modifications include 2′-fluoro, 2′-amino and 2′ O-methyl modifications on the ribose of pyrimidines, abasic residues or an inverted base at the 3′ end of the RNA. Such modifications are routinely incorporated into oligonucleotides and these oligonucleotides have been shown to have a higher Tm (i.e., higher target binding affinity) than 2′-deoxyoligonucleotides against a given target.

A number of nucleotide and nucleoside modifications have been shown to make the oligonucleotide into which they are incorporated more resistant to nuclease digestion than the native oligodeoxynucleotide; these modified oligos survive intact for a longer time than unmodified oligonucleotides. Specific examples of modified oligonucleotides include those comprising modified backbones, for example, phosphorothioates, phosphotriesters, methyl phosphonates, short chain alkyl or cycloalkyl intersugar linkages or short chain heteroatomic or heterocyclic intersugar linkages. Examples are oligonucleotides with phosphorothioate backbones and those with heteroatom backbones, particularly CH2-NH—O—CH2, CH, ˜N(CH3)˜O˜CH2 (known as a methylene(methylimino) or MMI backbone], CH2-O—N(CH3)-CH2, CH2-N(CH3)-N(CH3)-CH2 and O—N(CH3)-CH2-CH2 backbones, wherein the native phosphodiester backbone is represented as O—P—P—CH,); amide backbones (see De Mesmaeker et al. Ace. Chem. Res. 1995, 28:366-374); morpholino backbone structures (see Summerton and Weller, U.S. Pat. No. 5,034,506); peptide nucleic acid (PNA) backbone (wherein the phosphodiester backbone of the oligonucleotide is replaced with a polyamide backbone, the nucleotides being bound directly or indirectly to the aza nitrogen atoms of the polyamide backbone, see Nielsen et al., Science 1991, 254, 1497). Phosphorus-containing linkages include, but are not limited to, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates comprising 3′alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates comprising 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′; see U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455, 233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563, 253; 5,571,799; 5,587,361; and 5,625,050.

Morpholino-based oligomeric compounds are described in Dwaine A. Braasch and David R. Corey, Biochemistry, 2002, 41(14), 4503-4510); Genesis, volume 30, issue 3, 2001; Heasman, J., Dev. Biol., 2002, 243, 209-214; Nasevicius et al., Nat. Genet., 2000, 26, 216-220; Lacerra et al., Proc. Natl. Acad. Sci., 2000, 97, 9591-9596; and U.S. Pat. No. 5,034,506, issued Jul. 23, 1991. In some embodiments, the morpholino-based oligomeric compound is a phosphorodiamidate morpholino oligomer (PMO) (e.g., as described in Iverson, Curr. Opin. Mol. Ther., 3:235-238, 2001; and Wang et al., J. Gene Med., 12:354-364, 2010; the disclosures of which are incorporated herein by reference in their entireties).

Cyclohexenyl nucleic acid oligonucleotide mimetics are described in Wang et al., J. Am. Chem. Soc., 2000, 122, 8595-8602.

Modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These comprise those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH2 component parts; see U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5, 264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596, 086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439, each of which is herein incorporated by reference.

Modified oligonucleotides are also known that include oligonucleotides that are based on or constructed from arabinonucleotide or modified arabinonucleotide residues. Arabinonucleosides are stereoisomers of ribonucleosides, differing only in the configuration at the 2′-position of the sugar ring. In some embodiments, a 2′-arabino modification is 2′-F arabino. In some embodiments, the modified oligonucleotide is 2′-fluoro-D-arabinonucleic acid (FANA) (as described in, for example, Lon et al., Biochem., 41:3457-3467, 2002 and Min et al., Bioorg. Med. Chem. Lett., 12:2651-2654, 2002; the disclosures of which are incorporated herein by reference in their entireties). Similar modifications can also be made at other positions on the sugar, particularly the 3′ position of the sugar on a 3′ terminal nucleoside or in 2′-5′ linked oligonucleotides and the 5′ position of 5′ terminal nucleotide.

PCT Publication No. WO 99/67378 discloses arabinonucleic acids (ANA) oligomers and their analogues for improved sequence specific inhibition of gene expression via association to complementary messenger RNA.

Other modifications include ethylene-bridged nucleic acids (ENAs) (e.g., International Patent Publication No. WO 2005/042777, Morita et al., Nucleic Acid Res., Suppl 1:241-242, 2001; Surono et al., Hum. Gene Ther., 15:749-757, 2004; Koizumi, Curr. Opin. Mol. Ther., 8:144-149, 2006 and Horie et al., Nucleic Acids Symp. Ser (Oxf), 49:171-172, 2005; the disclosures of which are incorporated herein by reference in their entireties). Preferred ENAs include, but are not limited to, 2′-O,4′-C-ethylene-bridged nucleic acids.

Examples of LNAs are described in WO/2008/043753 and include compounds of the following formula.

where X and Y are independently selected among the groups —O—,

—S—, —N(H)—, N(R)—, —CH2- or —CH— (if part of a double bond),

—CH₂—O—, —CH₂—S—, —CH₂—N(H)—, —CH₂—N(R)—, —CH₂—CH₂— or —CH₂—CH— (if part of a double bond),

—CH═CH—, where R is selected from hydrogen and C₁₋₄-alkyl; Z and Z* are independently selected among an internucleoside linkage, a terminal group or a protecting group; B constitutes a natural or non-natural nucleotide base moiety; and the asymmetric groups may be found in either orientation.

Preferably, the LNA used in the oligomer of the invention comprises at least one LNA unit according any of the formulas

wherein Y is —O—, —S—, —NH—, or N(R^(H)); Z and Z* are independently selected among an internucleoside linkage, a terminal group or a protecting group; B constitutes a natural or non-natural nucleotide base moiety, and RH is selected from hydrogen and C₁₋₄-alkyl.

In some embodiments, the Locked Nucleic Acid (LNA) used in the oligomeric compound, such as an antisense oligonucleotide, of the invention comprises a Locked Nucleic Acid (LNA) unit according any of the formulas shown in Scheme 2 of PCT/DK2006/000512.

In some embodiments, the LNA used in the oligomer of the invention comprises internucleoside linkages selected from -0-P(O)₂—O—, —O—P(O,S)—O—, -0-P(S)₂—O—, —S—P(O)₂—O—, —S—P(O,S)—O—, —S—P(S)₂—O—, -0-P(O)₂—S—, —O—P(O,S)—S—, —S—P(O)₂—S—, —O—PO(R^(H))—O—, O—PO(OCH₃)—O—, —O—PO(NR^(H))—O—, -0-PO(OCH₂CH₂S—R)—O—, —O—PO(BH₃)—O—, —O—PO(NHR^(H))—O—, —O—P(O)₂—NR^(H)—, —NR^(H)—P(O)₂—O—, —NR^(H)—CO—O—, where R^(H) is selected from hydrogen and C₁₋₄-alkyl.

Certain examples of LNA units are shown in scheme 2:

The term “thio-LNA” comprises a locked nucleotide in which at least one of X or Y in the general formula above is selected from S or —CH2-S—. Thio-LNA can be in both beta-D and alpha-L-configuration.

The term “amino-LNA” comprises a locked nucleotide in which at least one of X or Y in the general formula above is selected from —N(H)—, N(R)—, CH₂—N(H)—, and —CH₂—N(R)— where R is selected from hydrogen and C₁₋₄-alkyl. Amino-LNA can be in both beta-D and alpha-L-configuration.

The term “oxy-LNA” comprises a locked nucleotide in which at least one of X or Y in the general formula above represents —O— or —CH₂—O—. Oxy-LNA can be in both beta-D and alpha-L-configuration.

The term “ena-LNA” comprises a locked nucleotide in which Y in the general formula above is —CH₂—O— (where the oxygen atom of —CH₂—O— is attached to the 2′-position relative to the base B).

LNAs are described in additional detail herein.

One or more substituted sugar moieties can also be included, e.g., one of the following at the 2′ position: OH, SH, SCH₃, F, OCN, OCH₃OCH₃, OCH₃O(CH₂)n CH₃, O(CH₂)n NH₂ or O(CH₂)n CH₃ where n is from 1 to about 10; C1 to C10 lower alkyl, alkoxyalkoxy, substituted lower alkyl, alkaryl or aralkyl; Cl; Br; CN; CF3; OCF3; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; SOCH3; SO2CH3; ONO2; NO2; N3; NH2; heterocycloalkyl; heterocycloalkaryl; amino alkylamino; polyalkylamino; substituted silyl; an RNA cleaving group; a reporter group; an intercalator; a group for improving the pharmacokinetic properties of an oligonucleotide; or a group for improving the pharmacodynamic properties of an oligonucleotide and other substituents having similar properties. An example modification includes 2′-methoxyethoxy[2′-O—CH₂CH₂OCH₃, also known as 2′-O-(2-methoxyethyl)] (Martin et al, HeIv. Chim. Acta, 1995, 78, 486). Other modifications include 2′-methoxy (2′-O—CH₃), 2′-propoxy (2′-OCH₂CH₂CH₃) and 2′-fluoro (2′-F). Similar modifications may also be made at other positions on the oligonucleotide, particularly the 3′ position of the sugar on the 3′ terminal nucleotide and the 5′ position of 5′ terminal nucleotide. Oligonucleotides may also have sugar mimetics such as cyclobutyls in place of the pentofuranosyl group.

Single stranded oligonucleotides can also include, additionally or alternatively, nucleobase (often referred to in the art simply as “base”) modifications or substitutions. As used herein, “unmodified” or “natural” nucleobases include adenine (A), guanine (G), thymine (T), cytosine (C) and uracil (U). Modified nucleobases include nucleobases found only infrequently or transiently in natural nucleic acids, e.g., hypoxanthine, 6-methyladenine, 5-Me pyrimidines, particularly 5-methylcytosine (also referred to as 5-methyl-2′ deoxycytosine and often referred to in the art as 5-Me-C), 5-hydroxymethylcytosine (HMC), glycosyl HMC and gentobiosyl HMC, isocytosine, pseudoisocytosine, as well as synthetic nucleobases, e.g., 2-aminoadenine, 2-(methylamino)adenine, 2-(imidazolylalkyl)adenine, 2-(aminoalklyamino)adenine or other heterosubstituted alkyladenines, 2-thiouracil, 2-thiothymine, 5-bromouracil, 5-hydroxymethyluracil, 5-propynyluracil, 8-azaguanine, 7-deazaguanine, N6 (6-aminohexyl)adenine, 6-aminopurine, 2-aminopurine, 2-chloro-6-aminopurine and 2,6-diaminopurine or other diaminopurines. See, e.g., Kornberg, “DNA Replication,” W. H. Freeman & Co., San Francisco, 1980, pp 75-77; and Gebeyehu, G., et al. Nucl. Acids Res., 15:4513 (1987)). A “universal” base known in the art, e.g., inosine, can also be included. 5-Me-C substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2<0>C. (Sanghvi, in Crooke, and Lebleu, eds., Antisense Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are example base substitutions.

It is not necessary for all positions in a given oligonucleotide to be uniformly modified, and in fact more than one of the modifications described herein may be incorporated in a single oligonucleotide or even at within a single nucleoside within an oligonucleotide.

In some embodiments, both a sugar and an internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an oligonucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, for example, an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative United States patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is herein incorporated by reference. Further teaching of PNA compounds can be found in Nielsen et al, Science, 1991, 254, 1497-1500.

Single stranded oligonucleotides can also include one or more nucleobase (often referred to in the art simply as “base”) modifications or substitutions. As used herein, “unmodified” or “natural” nucleobases comprise the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases comprise other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudo-uracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylquanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine.

Further, nucleobases comprise those disclosed in U.S. Pat. No. 3,687,808, those disclosed in “The Concise Encyclopedia of Polymer Science And Engineering”, pages 858-859, Kroschwitz, ed. John Wiley & Sons, 1990, those disclosed by Englisch et al., Angewandle Chemie, International Edition, 1991, 30, page 613, and those disclosed by Sanghvi, Chapter 15, Antisense Research and Applications,” pages 289-302, Crooke, and Lebleu, eds., CRC Press, 1993. Certain of these nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds of the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, comprising 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2<0>C (Sanghvi, et al., eds, “Antisense Research and Applications,” CRC Press, Boca Raton, 1993, pp. 276-278) and are example base substitutions, even more particularly when combined with 2′-O-methoxyethyl sugar modifications. Modified nucleobases are described in U.S. Pat. No. 3,687,808, as well as U.S. Pat. Nos. 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,596,091; 5,614,617; 5,750,692, and 5,681,941, each of which is herein incorporated by reference.

In some embodiments, the single stranded oligonucleotides are chemically linked to one or more moieties or conjugates that enhance the activity, cellular distribution, or cellular uptake of the oligonucleotide. For example, one or more single stranded oligonucleotides, of the same or different types, can be conjugated to each other; or single stranded oligonucleotides can be conjugated to targeting moieties with enhanced specificity for a cell type or tissue type. Such moieties include, but are not limited to, lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al, Ann. N. Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g., dodecandiol or undecyl residues (Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain (Mancharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or hexylamino-carbonyl-t oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923-937). See also U.S. Pat. Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762, 779; 4,789,737; 4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082, 830; 5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941, each of which is herein incorporated by reference.

These moieties or conjugates can include conjugate groups covalently bound to functional groups such as primary or secondary hydroxyl groups. Conjugate groups of the invention include intercalators, reporter molecules, polyamines, polyamides, polyethylene glycols, polyethers, groups that enhance the pharmacodynamic properties of oligomers, and groups that enhance the pharmacokinetic properties of oligomers. Typical conjugate groups include cholesterols, lipids, phospholipids, biotin, phenazine, folate, phenanthridine, anthraquinone, acridine, fluoresceins, rhodamines, coumarins, and dyes. Groups that enhance the pharmacodynamic properties, in the context of this invention, include groups that improve uptake, enhance resistance to degradation, and/or strengthen sequence-specific hybridization with the target nucleic acid. Groups that enhance the pharmacokinetic properties, in the context of this invention, include groups that improve uptake, distribution, metabolism or excretion of the compounds of the present invention. Representative conjugate groups are disclosed in International Patent Application No. PCT/US92/09196, filed Oct. 23, 1992, and U.S. Pat. No. 6,287,860, which are incorporated herein by reference. Conjugate moieties include, but are not limited to, lipid moieties such as a cholesterol moiety, cholic acid, a thioether, e.g., hexyl-5-tritylthiol, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl residues, a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or a polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl-oxy cholesterol moiety. See, e.g., U.S. Pat. Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941.

In some embodiments, single stranded oligonucleotide modification include modification of the 5′ or 3′ end of the oligonucleotide. In some embodiments, the 3′ end of the oligonucleotide comprises a hydroxyl group or a thiophosphate. It should be appreciated that additional molecules (e.g. a biotin moiety or a fluorophor) can be conjugated to the 5′ or 3′ end of the single stranded oligonucleotide. In some embodiments, the single stranded oligonucleotide comprises a biotin moiety conjugated to the 5′ nucleotide.

In some embodiments, the single stranded oligonucleotide comprises locked nucleic acids (LNA), ENA modified nucleotides, 2′-O-methyl nucleotides, or 2′-fluoro-deoxyribonucleotides. In some embodiments, the single stranded oligonucleotide comprises alternating deoxyribonucleotides and 2′-fluoro-deoxyribonucleotides. In some embodiments, the single stranded oligonucleotide comprises alternating deoxyribonucleotides and 2′-O-methyl nucleotides. In some embodiments, the single stranded oligonucleotide comprises alternating deoxyribonucleotides and ENA modified nucleotides. In some embodiments, the single stranded oligonucleotide comprises alternating deoxyribonucleotides and locked nucleic acid nucleotides. In some embodiments, the single stranded oligonucleotide comprises alternating locked nucleic acid nucleotides and 2′-O-methyl nucleotides.

In some embodiments, the 5′ nucleotide of the oligonucleotide is a deoxyribonucleotide. In some embodiments, the 5′ nucleotide of the oligonucleotide is a locked nucleic acid nucleotide. In some embodiments, the nucleotides of the oligonucleotide comprise deoxyribonucleotides flanked by at least one locked nucleic acid nucleotide on each of the 5′ and 3′ ends of the deoxyribonucleotides. In some embodiments, the nucleotide at the 3′ position of the oligonucleotide has a 3′ hydroxyl group or a 3′ thiophosphate.

In some embodiments, the single stranded oligonucleotide comprises phosphorothioate internucleotide linkages. In some embodiments, the single stranded oligonucleotide comprises phosphorothioate internucleotide linkages between at least two nucleotides. In some embodiments, the single stranded oligonucleotide comprises phosphorothioate internucleotide linkages between all nucleotides.

It should be appreciated that the single stranded oligonucleotide can have any combination of modifications as described herein.

The oligonucleotide may comprise a nucleotide sequence having one or more of the following modification patterns.

(a) (X)Xxxxxx, (X)xXxxxx, (X)xxXxxx, (X)xxxXxx, (X)xxxxXx and (X)xxxxxX,

-   -   (b) (X)XXxxxx, (X)XxXxxx, (X)XxxXxx, (X)XxxxXx, (X)XxxxxX,         (X)xXXxxx, (X)xXxXxx, (X)xXxxXx, (X)xXxxxX, (X)xxXXxx,         (X)xxXxXx, (X)xxXxxX, (X)xxxXXx, (X)xxxXxX and (X)xxxxXX,     -   (c) (X)XXXxxx, (X)xXXXxx, (X)xxXXXx, (X)xxxXXX, (X)XXxXxx,         (X)XXxxXx, (X)XXxxxX, (X)xXXxXx, (X)xXXxxX, (X)xxXXxX,         (X)XxXXxx, (X)XxxXXx (X)XxxxXX, (X)xXxXXx, (X)xXxxXX, (X)xxXxXX,         (X)xXxXxX and (X)XxXxXx,     -   (d) (X)xxXXX, (X)xXxXXX, (X)xXXxXX, (X)xXXXxX, (X)xXXXXx,         (X)XxxXXXX, (X)XxXxXX, (X)XxXXxX, (X)XxXXx, (X)XXxxXX,         (X)XXxXxX, (X)XXxXXx, (X)XXXxxX, (X)XXXxXx, and (X)XXXXxx,     -   (e) (X)xXXXXX, (X)XxXXXX, (X)XXxXXX, (X)XXXxXX, (X)XXXXxX and         (X)XXXXXx, and     -   (f) XXXXXX, XxXXXXX, XXxXXXX, XXXxXXX, XXXXxXX, XXXXXxX and         XXXXXXx, in which “X” denotes a nucleotide analogue, (X) denotes         an optional nucleotide analogue, and “x” denotes a DNA or RNA         nucleotide unit. Each of the above listed patterns may appear         one or more times within an oligonucleotide, alone or in         combination with any of the other disclosed modification         patterns.

Further Features of Oligonucleotides

Evidence is provided herein that such oligonucleotides increased expression of mRNA corresponding to the gene by at least about 50% (i.e. 150% of normal or 1.5 fold), or by about 2 fold to about 5 fold. In some embodiments it is contemplated that expression may be increased by at least about 15 fold, 20 fold, 30 fold, 40 fold, 50 fold or 100 fold, or any range between any of the foregoing numbers. In other experiments, increased mRNA expression has been shown to correlate to increased protein expression.

The sequence identifiers outlined in Table 2 refer to sequences of RNAs that associate (binds) with PRC2 (i.e., the RNA against which oligonucleotides would be directed) that are disclosed in International Patent Application Publication WO/2012/087983. Accordingly, each of the sequences comprise PRC2-associated regions. Each of (a) the reference genes described in the tables, (b) the PRC2 binding transcripts or Peaks (i.e., smaller regions of RNA that bind to PRC2) that target (modulate expression of) these genes, and (c) the oligonucleotides that specifically bind to, or are complementary to, the PRC2 binding transcripts or Peaks, may conveniently be grouped into any of these categories, represented by numbers in Table 3 of International Patent Application Publication WO/2012/087983 or represented by numbers in Table 9 of International Patent Application Publication WO/2012/065143 as follows: Diseases are marked by category numbers 11, 14, 15, 17, 21, 24, 26, 42, 44, 49, 58, 69, 82, 103, 119, 120, 126, 143, 163, 167, 172, 177, 182, 183, 184, 187, 191, 196, 200, 203, 204, 219, 220, 221, 227, 234, 239, 240, 244, 249, any one of 300-323, or any one of 400-643.

Other functional groups are marked by category numbers 10, 12, 13, 16, 18, 19, 20, 22, 23, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 43, 45, 46, 47, 48, 50, 51, 52, 54, 55, 56, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 102, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 121, 122, 123, 124, 125, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 158, 160, 161, 162, 164, 165, 166, 168, 169, 170, 171, 173, 174, 175, 176, 178, 179, 180, 181, 185, 186, 188, 189, 190, 192, 193, 194, 195, 197, 198, 199, 201, 202, 205, 206, 207, 208, 209, 210, 211, 213, 215, 216, 217, 218, 222, 223, 224, 226, 228, 229, 230, 231, 232, 233, 235, 236, 237, 238, 241, 242, 243, 245, 246, 247, 248, 250, 251, 252, or 253.

Category

No. Name 10 actin cytoskeleton organization 11 Acute myeloid leukemia 12 Adherens junction 13 Adipocytokine signaling pathway 14 aging 15 Alzheimer's disease 16 Amino sugar and nucleotide sugar metabolism 17 Amyotrophic lateral sclerosis (ALS) 18 angiogenesis 19 Apoptosis 20 Arginine and proline metabolism 21 Arrhythmogenic right ventricular cardiomyopathy (ARVC) 22 Axon guidance 23 B cell receptor signaling pathway 24 Basal cell carcinoma, also in category 644 25 Basal transcription factors 26 Bladder cancer, also in category 644 27 blood coagulation 28 blood vessel development 29 bone development 30 Calcium signaling pathway 31 Cardiac muscle contraction 32 cation channel activity 33 cell adhesion 34 cell cycle 35 Cell cycle 36 cell motion 37 cell surface receptor linked signal transduction 38 cellular response to stress 39 channel activity 40 Chemokine signaling pathway 41 cholesterol metabolic process 42 Chronic myeloid leukemia 43 Citrate cycle (TCA cycle) 44 Colorectal cancer 45 Complement and coagulation cascades 46 cytokine activity 47 cyto skeletal protein binding 48 cytosol 49 Dilated cardiomyopathy 50 DNA binding 51 DNA repair 52 DNA replication 53 DNA replication 54 Drug metabolism 55 embryonic morphogenesis 56 endocytosis 57 Endocytosis 58 Endometrial cancer 59 endoplasmic reticulum 60 ErbB signaling pathway 61 extracellular region 62 eye development 63 Fatty acid metabolism 64 Fructose and mannose metabolism 65 G-protein coupled receptor protein signaling pathway 66 gamete generation 67 Gap junction 68 gene silencing by miRNA 69 Glioma 70 glucose metabolic process 71 Glycolysis/Gluconeogenesis 72 Golgi apparatus 73 growth factor activity 74 GTPase regulator activity 75 heart development 76 Hedgehog signaling pathway 77 Hematopoietic cell lineage 78 hemopoiesis 79 hemopoietic or lymphoid organ development 80 histone modification 81 Huntington's disease 82 Hypertrophic cardiomyopathy (HCM) 83 immune response 84 immune system development 85 inflammatory response 86 Insulin signaling pathway 87 intracellular signaling cascade 88 ion channel activity 89 ion transport 90 Jak-STAT signaling pathway 91 learning or memory 92 leukocyte activation 93 Leukocyte transendothelial migration 94 limb development 95 locomotory behavior 96 Long-term potentiation 97 lung development 98 lysosome 99 Lysosome 100 MAPK signaling pathway 101 MAPKKK cascade 102 Melanogenesis 103 Melanoma 104 Mismatch repair 105 mitochondrion 106 mitochondrion organization 107 mTOR signaling pathway 108 muscle tissue development 109 ncRNA metabolic process 110 neuron development 111 Neurotrophin signaling pathway 112 Non-small cell lung cancer, also in category 644 113 Notch signaling pathway 114 nucleolus 115 Oocyte meiosis 116 oxidation reduction 117 Oxidative phosphorylation 118 p53 signaling pathway 119 Pancreatic cancer, also in category 644 120 Parkinson's disease 121 Pathways in cancer, also in category 644 122 phosphatase activity 123 phosphoprotein phosphatase activity 124 positive regulation of cellular biosynthetic process 125 PPAR signaling pathway 126 Prostate cancer, also in category 644 127 Proteasome 128 protein amino acid dephosphorylation 129 protein folding 130 protein kinase activity 131 protein serine/threonine kinase activity 132 Purine metabolism 133 Pyrimidine metabolism 134 Ras protein signal transduction 135 Regulation of actin cytoskeleton 136 Regulation of autophagy 137 regulation of cell death, also in category 644 138 regulation of cell proliferation, also in category 644 139 regulation of cell size 140 regulation of protein ubiquitination 141 regulation of Ras protein signal transduction 142 regulation of transcription 143 Renal cell carcinoma, also in category 644 144 response to hypoxia 145 response to steroid hormone stimulus 146 response to virus 147 ribosome 148 RNA degradation 149 RNA processing 150 RNA splicing, via transesterification reactions 151 secretion 152 skeletal system development 153 skeletal system morphogenesis 154 Small cell lung cancer, also in category 644 155 small GTPase regulator activity 156 spermatogenesis 157 Sphingolipid metabolism 158 spliceosome 159 Spliceosome 160 stem cell differentiation 161 Steroid biosynthesis 162 synapse 163 Systemic lupus erythematosus 164 T cell activation 165 T cell receptor signaling pathway 166 TGF-beta signaling pathway 167 Thyroid cancer, also in category 644 168 Toll-like receptor signaling pathway 169 transcription activator activity 170 transcription factor activity 171 translation 172 Type II diabetes mellitus 173 Ubiquitin mediated proteolysis 174 Vascular smooth muscle contraction 175 vasculature development 176 VEGF signaling pathway 177 Viral myocarditis 178 Wnt signaling pathway 179 amino-acid biosynthesis 180 ank repeat 181 bromodomain 182 Cardiomyopathy 183 cataract 184 charcot-marie-tooth disease 185 cytokine 186 cytokine receptor 187 deafness 188 disease mutation 189 egf-like domain 190 endosome 191 epilepsy 192 glycoprotein 193 growth factor 194 Growth factor binding 195 growth factor receptor 196 Ichthyosis 197 Immunoglobulin domain 198 ionic channel 199 leucine-rich repeat 200 leukodystrophy 201 methylation 202 methyltransferase 203 neurodegeneration 204 neuropathy 205 nucleus 206 obesity 207 protein phosphatase 208 protein phosphatase inhibitor 209 Oncogene (including proto-oncogenes), also in category 644 210 Secreted 211 serine/threonine-specific protein kinase 212 systemic lupus erythematosus 213 transmembrane 214 transmembrane protein 215 tumor suppressor, also in category 644 216 tyrosine-protein kinase 217 ubl conjugation pathway 218 wd repeat 300 Downregulated in Bladder cancer, also in category 644 301 Downregulated in Leukemia, also in category 644 302 Downregulated in Brain cancer, also in category 644 303 Downregulated in Breast cancer, also in category 644 304 Downregulated in Cervical cancer, also in category 644 305 Downregulated in Colon cancer, also in category 644 306 Downregulated in Esophageal cancer, also in category 644 307 Downregulated in Gastric cancer, also in category 644 308 Downregulated in Head and Neck cancer, also in category 644 309 Downregulated in Renal cancer, also in category 644 310 Downregulated in Liver cancer, also in category 644 311 Downregulated in Lung cancer, also in category 644 312 Downregulated in Lymphoma, also in category 644 313 Downregulated in Melanoma, also in category 644 314 Downregulated in Multiple Myeloma, also in category 644 315 Downregulated in Ovarian cancer, also in category 644 316 Downregulated in Pancreatic cancer, also in category 644 317 Downregulated in Prostate cancer, also in category 644 318 Downregulated in Sarcoma, also in category 644 319 Downregulated in Non-melanoma skin cancer, also in category 644 320 Downregulated in Uterine cancer, also in category 644 321 Downregulated in Mesothelioma, also in category 644 322 Downregulated in Adrenal cancer, also in category 644 323 Downregulated in Parathyroid cancer, also in category 644 400 Upregulated in Clear cell sarcoma of kidney, also in category 644 401 Upregulated in Acute lung injury 402 Upregulated in Acute megakaryoblastic leukemia, also in category 644 403 Upregulated in Acute myelocytic leukemia, also in category 644 404 Upregulated in Acute pancreatitis unspecified 405 Upregulated in Adenocarcinoma of esophagus, also in category 644 406 Upregulated in Adenocarcinoma of lung, also in category 644 407 Upregulated in Adenoma of small intestine, also in category 644 408 Upregulated in Adenovirus infection 409 Upregulated in AIDS with encephalitis 410 Upregulated in Alcohol poisoning 411 Upregulated in Alexander disease 412 Upregulated in alpha-1-Antitrypsin deficiency 413 Upregulated in Alzheimer's disease 414 Upregulated in Anaplastic oligoastrocytoma, also in category 644 415 Upregulated in Androgen insensitivity syndrome 416 Upregulated in Astrocytoma, also in category 644 417 Upregulated in Atrophy-muscular 418 Upregulated in Autoimmune hepatitis 419 Upregulated in Bacterial infection 420 Upregulated in Barrett's esophagus 421 Upregulated in Carcinoma in situ of small intestin, also in category 644e 422 Upregulated in Cardiomyopathy 423 Upregulated in Chronic granulomatous disease 424 Upregulated in Chronic lymphocytic leukemia 425 Upregulated in Chronic obstructive airway disease 426 Upregulated in Chronic polyarticular juvenile rheumatoid arthritis 427 Upregulated in Cirrhosis of liver 428 Upregulated in Cocaine dependence 429 Upregulated in Complex dental caries 430 Upregulated in Crohn's disease 431 Upregulated in Decompensated cardiac failure 432 Upregulated in Dehydration 433 Upregulated in Dilated cardiomyopathy 434 Upregulated in Dilated cardiomyopathy secondary to viral myocarditis 435 Upregulated in Epithelial proliferation 436 Upregulated in Escherichia coli infection of the central nervous system 437 Upregulated in Essential thrombocythemia 438 Upregulated in Exhaustion due to excessive exertion 439 Upregulated in Familial hypophosphatemic bone disease 440 Upregulated in Fracture 441 Upregulated in Fracture of femur 442 Upregulated in Generalized ischemic myocardial dysfunction 443 Upregulated in Glioblastoma, also in category 644 444 Upregulated in Hamman-Rich syndrome 445 Upregulated in Helicobacter pylori gastrointestinal tract infection 446 Upregulated in Hepatitis C 447 Upregulated in HIV infection 448 Upregulated in Huntington's disease 449 Upregulated in Hypercholesterolemia 450 Upregulated in Hypertrophy 451 Upregulated in Idiopathic thrombocytopenic purpura 452 Upregulated in Infection by Yersinia enterocolitica 453 Upregulated in Infertility due to azoospermia 454 Upregulated in Injury of heart 455 Upregulated in ISM-In situ melanoma of skin 456 Upregulated in Leber's amaurosis 457 Upregulated in Liver carcinoma, also in category 644 458 Upregulated in Macular degeneration 459 Upregulated in Malignant lymphoma, also in category 644 460 Upregulated in Malignant neoplasm of cervix uteri, also in category 644 461 Upregulated in Malignant neoplasm of duodenum, also in category 644 462 Upregulated in Malignant neoplasm of prostate, also in category 644 463 Upregulated in Malignant neoplasm of stomach, also in category 644 464 Upregulated in Malignant neoplasm of testis, also in category 644 465 Upregulated in Malignant tumor of colon, also in category 644 466 Upregulated in Multiple benign melanocytic nevi 467 Upregulated in Nephropathy-diabetic 468 Upregulated in Non-insulin dependent diabetes mellitus 469 Upregulated in Nutritional deficiency 470 Upregulated in Obstructive sleep apnea 471 Upregulated in Oligodendroglioma, also in category 644 472 Upregulated in Papillary thyroid carcinoma, also in category 644 473 Upregulated in Parkinson disease 474 Upregulated in Porcine nephropathy 475 Upregulated in Pre-eclampsia 476 Upregulated in Primary cardiomyopathy 477 Upregulated in Primary open angle glaucoma 478 Upregulated in Primary pulmonary hypoplasia 479 Upregulated in Pseudomonas infection 480 Upregulated in Pulmonary emphysema 481 Upregulated in Pulmonary hypertension 482 Upregulated in Renal disorder associated with type II diabetes mellitus 483 Upregulated in Retinal damage 484 Upregulated in Retinitis pigmentosa 485 Upregulated in Rheumatoid arthritis 486 Upregulated in Squamous cell carcinoma, also in category 644 487 Upregulated in Squamous cell carcinoma of lung, also in category 644 488 Upregulated in Status epilepticus 489 Upregulated in Systemic infection 490 Upregulated in Thrombocytopenia 491 Upregulated in Thymic carcinoma, also in category 644 492 Upregulated in Transitional cell carcinoma, also in category 644 493 Upregulated in Transitional cell carcinoma in situ, also in category 644 494 Upregulated in Ulcerative colitis 495 Upregulated in Uterine fibroids 496 Upregulated in Ventilator-associated lung injury 497 Upregulated in Ventricular hypertrophy 498 Upregulated in Ventricular hypertrophy (& [left]) 499 Upregulated in Vitamin A deficiency 500 Downregulated in Clear cell sarcoma of kidney, also in category 644 501 Downregulated in Acute lung injury 502 Downregulated in Acute megakaryoblastic leukemia, also in category 644 503 Downregulated in Acute myelocytic leukemia, also in category 644 504 Downregulated in Acute pancreatitis unspecified 505 Downregulated in Adenocarcinoma of esophagus, also in category 644 506 Downregulated in Adenocarcinoma of lung, also in category 644 507 Downregulated in Adenoma of small intestine, also in category 644 508 Downregulated in Adenovirus infection 509 Downregulated in AIDS with encephalitis 510 Downregulated in Alcohol poisoning 511 Downregulated in Alexander disease 512 Downregulated in alpha-1-Antitrypsin deficiency 513 Downregulated in Alzheimer's disease 514 Downregulated in Anaplastic oligoastrocytoma 515 Downregulated in Androgen insensitivity syndrome 516 Downregulated in Astrocytoma, also in category 644 517 Downregulated in Atrophy-muscular 518 Downregulated in Autoimmune hepatitis 519 Downregulated in Bacterial infection 520 Downregulated in Barrett's esophagus 521 Downregulated in Carcinoma in situ of small intestine, also in category 644 522 Downregulated in Cardiomyopathy 523 Downregulated in Chronic granulomatous disease 524 Downregulated in Chronic lymphocytic leukemia 525 Downregulated in Chronic obstructive airway disease 526 Downregulated in Chronic polyarticular juvenile rheumatoid arthritis 527 Downregulated in Cirrhosis of liver 528 Downregulated in Cocaine dependence 529 Downregulated in Complex dental caries 530 Downregulated in Crohn's disease 531 Downregulated in Decompensated cardiac failure 532 Downregulated in Dehydration 533 Downregulated in Dilated cardiomyopathy 534 Downregulated in Dilated cardiomyopathy secondary to viral myocarditis 535 Downregulated in Epithelial proliferation 536 Downregulated in Escherichia coli infection of the central nervous system 537 Downregulated in Essential thrombocythemia 538 Downregulated in Exhaustion due to excessive exertion 539 Downregulated in Familial hypophosphatemic bone disease 540 Downregulated in Fracture 541 Downregulated in Fracture of femur 542 Downregulated in Generalized ischemic myocardial dysfunction 543 Downregulated in Glioblastoma, also in category 644 544 Downregulated in Hamman-Rich syndrome 545 Downregulated in Helicobacter pylori gastrointestinal tract infection 546 Downregulated in Hepatitis C 547 Downregulated in HIV infection 548 Downregulated in Huntington's disease 549 Downregulated in Hypercholesterolemia 550 Downregulated in Hypertrophy 551 Downregulated in Idiopathic thrombocytopenic purpura 552 Downregulated in Infection by Yersinia enterocolitica 553 Downregulated in Infertility due to azoospermia 554 Downregulated in Injury of heart 555 Downregulated in ISM-In situ melanoma of skin, also in category 644 556 Downregulated in Leber's amaurosis 557 Downregulated in Liver carcinoma, also in category 644 558 Downregulated in Macular degeneration 559 Downregulated in Malignant lymphoma, also in category 644 560 Downregulated in Malignant neoplasm of cervix uteri, also in category 644 561 Downregulated in Malignant neoplasm of duodenum, also in category 644 562 Downregulated in Malignant neoplasm of prostate, also in category 644 563 Downregulated in Malignant neoplasm of stomach, also in category 644 564 Downregulated in Malignant neoplasm of testis, also in category 644 565 Downregulated in Malignant tumor of colon, also in category 644 566 Downregulated in Multiple benign melanocytic nevi 567 Downregulated in Nephropathy-diabetic 568 Downregulated in Non-insulin dependent diabetes mellitus 569 Downregulated in Nutritional deficiency 570 Downregulated in Obstructive sleep apnea 571 Downregulated in Oligodendroglioma 572 Downregulated in Papillary thyroid carcinoma 573 Downregulated in Parkinson disease 574 Downregulated in Porcine nephropathy 575 Downregulated in Pre-eclampsia 576 Downregulated in Primary cardiomyopathy 577 Downregulated in Primary open angle glaucoma 578 Downregulated in Primary pulmonary hypoplasia 579 Downregulated in Pseudomonas infection 580 Downregulated in Pulmonary emphysema 581 Downregulated in Pulmonary hypertension 582 Downregulated in Renal disorder associated with type II diabetes mellitus 583 Downregulated in Retinal damage 584 Downregulated in Retinitis pigmentosa 585 Downregulated in Rheumatoid arthritis 586 Downregulated in Squamous cell carcinoma, also in category 644 587 Downregulated in Squamous cell carcinoma of lung, also in category 644 588 Downregulated in Status epilepticus 589 Downregulated in Systemic infection 590 Downregulated in Thrombocytopenia 591 Downregulated in Thymic carcinoma, also in category 644 592 Downregulated in Transitional cell carcinoma, also in category 644 593 Downregulated in Transitional cell carcinoma in situ, also in category 644 594 Downregulated in Ulcerative colitis 595 Downregulated in Uterine fibroids 596 Downregulated in Ventilator-associated lung injury 597 Downregulated in Ventricular hypertrophy 598 Downregulated in Ventricular hypertrophy (& [left]) 599 Downregulated in Vitamin A deficiency 600 is associated with Bone diseases 601 is associated with Cancer diseases, also in category 644 602 is associated with Cardiovascular diseases 603 is associated with Connective tissue disorder diseases 604 is associated with Dermatological diseases 605 is associated with Developmental diseases 606 is associated with Ear, Nose, Throat diseases 607 is associated with Endocrine diseases 608 is associated with Gastrointestinal diseases 609 is associated with Hematological diseases 610 is associated with Immunological diseases 611 is associated with Metabolic diseases 612 is associated with multiple diseases 613 is associated with Muscular diseases 614 is associated with Neurological diseases 615 is associated with Nutritional diseases 616 is associated with Ophthamological diseases 617 is associated with Other diseases 618 is associated with Psychiatric diseases 619 is associated with Renal diseases 620 is associated with Respiratory diseases 621 is associated with Skeletal diseases 622 is decreased in Bone diseases 623 is decreased in Cancer diseases, also in category 644 624 is decreased in Cardiovascular diseases 625 is decreased in Connective tissue disorder diseases 626 is decreased in Dermatological diseases 627 is decreased in Developmental diseases 628 is decreased in Ear, Nose, Throat diseases 629 is decreased in Endocrine diseases 630 is decreased in Gastrointestinal diseases 631 is decreased in Hematological diseases 632 is decreased in Immunological diseases 633 is decreased in Metabolic diseases 634 is decreased in multiple diseases 635 is decreased in Muscular diseases 636 is decreased in Neurological diseases 637 is decreased in Nutritional diseases 638 is decreased in Ophthamological diseases 639 is decreased in Other diseases 640 is decreased in Psychiatric diseases 641 is decreased in Renal diseases 642 is decreased in Respiratory diseases 643 is decreased in Skeletal diseases 644 is involved in cancer

Thus, in various aspects, the invention features oligonucleotides that specifically bind to any of the RNA sequences disclosed herein, for use in modulating expression of genes. In another aspect, the invention also features oligonucleotides that specifically bind, or are complementary, to any of the RNA sequences of sequences B47,408 to B616,428 [mouse Peaks] or B652,256 to B916,209 [human Peaks] or B916,626 to B934,7619-[longer region surrounding human Peaks], whether in the “opposite strand” or the “same strand” as a target gene (e.g., as indicated in Table 2 of International Patent Application Publication WO/2012/087983). In some embodiments, the oligonucleotide is provided for use in a method of modulating expression of a gene targeted by the PRC2 binding RNA (e.g., an intersecting or nearby gene). Such methods may be carried out in vitro, ex vivo, or in vivo. In some embodiments, the oligonucleotide is provided for use in methods of treating disease. The treatments may involve modulating expression of a gene targeted by the PRC2 binding RNA, preferably upregulating gene expression. In some embodiments, the oligonucleotide is formulated as a sterile composition for parenteral administration. The reference genes targeted by these RNA sequences are set forth in Tables 2-3 and are grouped according to categories 1-644 in Table 3 of International Patent Application Publication WO/2012/087983 or are imprinted genes set forth in Table 2. Thus, in one aspect the invention describes a group of oligonucleotides that specifically bind, or are complementary to, a group of RNA sequences, either transcripts or Peaks, in any one of categories 1-644. In particular, the invention features uses of such oligonucleotides to upregulate expression of any of the reference genes set forth in Tables 2, for use in treating a disease, disorder, condition or association described in any of the categories set forth in Table 3 of International Patent Application Publication WO/2012/087983 (e.g., any one or more of category numbers 11, 14, 15, 17, 21, 24, 26, 42, 44, 49, 58, 69, 82, 103, 119, 120, 126, 143, 163, 167, 172, 177, 182, 183, 184, 187, 191, 196, 200, 203, 204, 212, 300 323, and/or 400-644).

By way of non-limiting example, category 45 (Complement and coagulation cascades) includes reference genes selected from the group consisting of A2M, SERPINC1, BDKRB1, BDKRB2, CFB, SERPING1, C1QA, C1QB, C1QC, C1R, C1S, C2, C3, C3AR1, C4A, C4B, C4BPA, C4BPB, C5, C5AR1, C6, C7, C8A, C8B, C9, CD59, CPB2, CR1, CR2, CD55, CFD, F2, F3, F5, F7, F8, F9, F10, F11, F12, F13A1, F13B, FGA, FGB, FGG, SERPIND1, CFH, CFI, KLKB1, KNG1, MBL2, CD46, SERPINE1, SERPINA1, PLAT, PLAU, PLAUR, PLG, SERPINF2, PROC, PROS1, MASP1, TFPI, THBD, VWF and/or MASP2.

In turn, each of A2M, SERPINC1, BDKRB1, BDKRB2, CFB, SERPING1, C1QA, C1QB, C1QC, C1R, C1S, C2, C3, C3AR1, C4A, C4B, C4BPA, C4BPB, C5, C5AR1, C6, C7, C8A, C8B, C9, CD59, CPB2, CR1, CR2, CD55, CFD, F2, F3, F5, F7, F8, F9, F10, F11, F12, F13A1, F13B, FGA, FGB, FGG, SERPIND1, CFH, CFI, KLKB1, KNG1, MBL2, CD46, SERPINE1, SERPINA1, PLAT, PLAU, PLAUR, PLG, SERPINF2, PROC, PROS1, MASP1, TFPI, THBD, VWF and/or MASP2 are targeted by PRC2-associated RNA having the sequence identifiers displayed in the applicable row of Table 2 of International Patent Application Publication WO/2012/087983. For example, F2 targeting sequences include sequences: B620037 [F], B620035 [4027], B790730 [4752], B4539 [2059], B341288 [3278], B4537 [4639] on the same strand as the coding gene, and sequences: B620036 [F], B790731-[F], B4538 [F], B341286 [F], B341287 [F] on the opposite strand from the coding gene, according to Table 2 of International Patent Application Publication WO/2012/087983.

The group of oligonucleotides that specifically bind to, or are complementary to, any one of these sequences that are listed in Table 2 of International Patent Application Publication WO/2012/087983 as targeting refGenes A2M, SERPINC1, BDKRB1, BDKRB2, CFB, SERPING1, C1QA, C1QB, C1QC, C1R, C1S, C2, C3, C3AR1, C4A, C4B, C4BPA, C4BPB, C5, C5AR1, C6, C7, C8A, C8B, C9, CD59, CPB2, CR1, CR2, CD55, CFD, F2, F3, F5, F7, F8, F9, F10, F11, F12, F13A1, F13B, FGA, FGB, FGG, SERPIND1, CFH, CFI, KLKB1, KNG1, MBL2, CD46, SERPINE1, SERPINA1, PLAT, PLAU, PLAUR, PLG, SERPINF2, PROC, PROS1, MASP1, TFPI, THBD, VWF and/or MASP2 are contemplated for use in any of the compositions and methods described herein, including but not limited to use in treating a disease of category 45 (Complement and coagulation cascades), the treatment involving modulation of any of the refGenes A2M, SERPINC1, BDKRB1, BDKRB2, CFB, SERPING1, C1QA, C1QB, C1QC, C1R, CIS, C2, C3, C3AR1, C4A, C4B, C4BPA, C4BPB, C5, C5AR1, C6, C7, C8A, C8B, C9, CD59, CPB2, CR1, CR2, CD55, CFD, F2, F3, F5, F7, F8, F9, F10, F11, F12, F13A1, F13B, FGA, FGB, FGG, SERPIND1, CFH, CFI, KLKB1, KNG1, MBL2, CD46, SERPINE1, SERPINA1, PLAT, PLAU, PLAUR, PLG, SERPINF2, PROC, PROS1, MASP1, TFPI, THBD, VWF and/or MASP2.

Similarly, oligonucleotides that specifically bind to, or are complementary to, genes in category 643 (“is decreased in Skeletal disease”) are contemplated for use in any of the compositions and methods described herein, including but not limited to use in treating Skeletal disease. Oligonucleotides that specifically bind to, or are complementary to, genes in the categories that are also part of category 644 (involved in cancer) are contemplated for use in any of the compositions and methods described herein, including but not limited to use in treating cancer.

It is understood that oligonucleotides of the invention may be complementary to, or specifically bind to, Peaks, or non-Peak regions of transcripts disclosed herein, or regions adjacent to Peaks. In various aspects, the invention also features oligonucleotides that bind to the RNA sequence between two or more Peaks that correspond to chromosomal coordinates that are near each other, e.g., within 100 bases, 200 bases, 300 bases, 400 bases, 500 bases, 1 kb, or 2 kb, of each other, and that are preferably associated with the same reference gene in Table 8 of International Patent Application Publication WO/2012/065143 or Table 2 of International Patent Application: PCT/US2011/65939. For example, the invention features oligonucleotides that specifically bind, or are complementary to, a fragment of any of the RNA transcripts of sequences A1 to A21582 or A191089 to A193049 or B1 to B47,407 or B934,762 to B934,863[mouse transcripts] or B616,429 to B652,255 or B916,210 to B916,625 or B934,864 to B934,968 [human transcripts] or B916,626 to B934,761 [larger region surrounding human Peaks], said fragment about 2000, about 1750, about 1500, about 1250 nucleotides in length, or preferably about 1000, about 750, about 500, about 400, about 300 nucleotides in length, or more preferably about 200, about 150, or about 100 nucleotides in length, wherein the fragment of RNA comprises a stretch of at least five (5) consecutive nucleotides within any of sequences A124437 to A190716, or A190934 to A191086, or A191087 [human Peaks], or sequences A21583 to A124436, or A190717 to 190933, or 191088 [mouse Peaks], or sequences B47,408 to B616,428 [mouse Peaks] or sequences B652,256 to B916,209 [human Peaks], or the reverse complement of any of the cDNA sequences of Appendix I of U.S. Prov. Appl. No. 61/425,174 filed on Dec. 20, 2010, which is incorporated by reference herein in its entirety. In exemplary embodiments the fragment of RNA comprises at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 or 50 consecutive nucleotides within any of sequences A124437 to A190716, or A190934 to A191086, or A191087 [human Peaks], or sequences A21583 to A124436, or A190717 to A190933, or A191088 [mouse Peaks], or sequences B47,408 to B616,428 [mouse Peaks] or sequences B652,256 to B916,209 [human Peaks], or the reverse complement of any of the cDNA sequences of Appendix I of U.S. Prov. Appl. No. 61/425,174 filed on Dec. 20, 2010.

Thus, for example, this description includes oligonucleotides that bind to fragments about 2000, about 1750, about 1500, about 1250 nucleotides in length, or preferably about 1000, about 750, about 500, about 400, about 300 nucleotides in length, or more preferably about 200, about 150, or about 100 nucleotides in length, which are:

(a) fragments of any of sequences B1-B47407 [mouse transcripts] that comprise a stretch of at least five (5) consecutive nucleotides, or 6, 7, 8, 9 or 10 or more consecutive nucleotides, within any of sequences B47408-B616428 [mouse Peaks], preferably associated with the same reference gene in Table 2 of International Patent Application Publication WO/2012/087983;

(b) fragments of any of sequences B616429-B652255 [human transcripts] that comprise a stretch of at least five (5) consecutive nucleotides, or 6, 7, 8, 9 or 10 or more consecutive nucleotides, within any of sequences B652256-B916209 [human Peaks], preferably associated with the same reference gene in Table 2 of International Patent Application Publication WO/2012/087983;

(c) fragments of any of sequences B916626-B934761-[longer regions around human Peaks] that comprise a stretch of at least five (5) consecutive nucleotides, or 6, 7, 8, 9 or 10 or more consecutive nucleotides, within any of sequences B652256-B916209 [human Peaks], preferably associated with the same reference gene in Table 2 of International Patent Application Publication WO/2012/087983;

(d) fragments of any of sequences B934762-B934863 [mouse imprinted transcripts] that encompass that comprise a stretch of at least five (5) consecutive nucleotides, or 6, 7, 8, 9 or 10 or more consecutive nucleotides, within any of sequences B47408-B616428 [mouse Peaks], preferably associated with the same reference gene in Table 2 of International Patent Application Publication WO/2012/087983 or Table 2;

(e) fragments of any of sequences B629991, B629992, B630983, B630984, B630990, B631003, B631004, B632396, B632397, B632402, B632403, B632419, B632422, B634959, B638303, B638304, B647595, B647596, B647597, B647598, B647601, B649028, and B934864-B934931-[human imprinted transcripts] that comprise a stretch of at least five (5) consecutive nucleotides, or 6, 7, 8, 9 or 10 or more consecutive nucleotides, within any of sequences B652256-B916209 [human Peaks], preferably associated with the same reference gene in Table 2 of International Patent Application Publication WO/2012/087983 or Table 2;

(f) fragments of any of sequences B916210-B916625 [human transcripts] that comprise a stretch of at least five (5) consecutive nucleotides, or 6, 7, 8, 9 or 10 or more consecutive nucleotides, within any of sequences B652256-B916209 [human Peaks], preferably associated with the same reference gene in Table 2 of International Patent Application Publication WO/2012/087983; or

(g) fragments of any of sequences B934932-B934968 [human transcripts] that comprise a stretch of at least five (5) consecutive nucleotides, or 6, 7, 8, 9 or 10 or more consecutive nucleotides, within any of sequences B652256-B916209 [human Peaks], preferably associated with the same reference gene in Table 2 of International Patent Application Publication WO/2012/087983.

Thus, as noted above, the oligonucleotide can comprise or consist of a sequence of bases at least 80% complementary to at least 10, or 10-30 or 10-40 contiguous bases of the target RNA, or at least 80% complementary to at least 15, or 15-30, or 15-40 contiguous bases of the target RNA, or at least 80% complementary to at least 20, or 20-30, or 20-40 contiguous bases of the target RNA, or at least 80% complementary to at least 25, or 25-30, or 25-40 contiguous bases of the target RNA, or at least 80% complementary to at least 30, or 30-40 contiguous bases of the target RNA, or at least 80% complementary to at least 40 contiguous bases of the target RNA. Moreover, the oligonucleotide can comprise or consist of a sequence of bases at least 90% complementary to at least 5, or 5-30 or 5-40 or 8-40 contiguous bases of the target RNA, or at least 90% complementary to at least 10, or 10-30, or 10-40 contiguous bases of the target RNA, or at least 90% complementary to at least 15, or 15-30, or 15-40 contiguous bases of the target RNA, or at least 90% complementary to at least 20, or 20-30, or 20-40 contiguous bases of the target RNA, or at least 90% complementary to at least 25, or 25-30, or 25-40 contiguous bases of the target RNA, or at least 90% complementary to at least 30, or 30-40 contiguous bases of the target RNA, or at least 90% complementary to at least 40 contiguous bases of the target RNA. Similarly, the oligonucleotide can comprise or consist of a sequence of bases fully complementary to at least 5, 10, or 15 contiguous bases of the target RNA. It is understood that some additional non complementary bases may be included. It is understood that oligonucleotides that comprise such sequences of bases as described may also comprise other non-complementary bases. For example, an oligonucleotide can be 20 bases in total length but comprise a 15 base portion that is fully complementary to 15 bases of the target RNA. Similarly, an oligonucleotide can be 20 bases in total length but comprise a 15 base portion that is at least 80% complementary to 15 bases of the target RNA.

Complementarity can also be referenced in terms of the number of mismatches in complementary base pairing, as noted above. Thus, the oligonucleotide can comprise or consist of a sequence of bases with up to 3 mismatches over 10 contiguous bases of the target RNA, or up to 3 mismatches over 15 contiguous bases of the target RNA, or up to 3 mismatches over 20 contiguous bases of the target RNA, or up to 3 mismatches over 25 contiguous bases of the target RNA, or up to 3 mismatches over 30 contiguous bases of the target RNA. Similarly, the oligonucleotide can comprise or consist of a sequence of bases with up to 2 mismatches over 10 contiguous bases of the target RNA, or up to 2 mismatches over 15 contiguous bases of the target RNA, or up to 2 mismatches over 20 contiguous bases of the target RNA, or up to 2 mismatches over 25 contiguous bases of the target RNA, or up to 2 mismatches over 30 contiguous bases of the target RNA. Similarly, the oligonucleotide can comprise or consist of a sequence of bases with one mismatch over 10, 15, 20, 25 or 30 contiguous bases of the target RNA.

In some or any of the embodiments of oligonucleotides described herein (e.g., in the summary, detailed description, or examples of embodiments) or the processes for designing or synthesizing them, the oligonucleotides may optionally exclude any one or more of the oligonucleotides as disclosed in any one or more of the following publications: as target HOTAIR RNA (Rinn et al., 2007), Tsix, RepA, or Xist RNAs ((Zhao et al., 2008) [sequences B936166-B936170], or (Sarma et al., 2010) [sequences B936177-B936186] or (Zhao et al., 2010) [sequences B936187-B936188] or (Prasnath et al., 2005) [sequences B936173-B936176]. or (Shamovsky et al., 2006) [sequence B936172] or (Mariner et al., 2008) [sequence B936171] or (Sunwoo et al., 2008) or (Bernard et al., 2010) [sequence B936189]; or as targeting short RNAs of 50 200 nt that are identified as candidate PRC2 regulators (Kanhere et al., 2010); or (Kuwabara et al., US 2005/0226848) [sequences B936190-B936191] or (Li et al., US 2010/0210707) [sequences B936192-B936227] or (Corey et al., U.S. Pat. No. 7,709,456) [sequences B936228-B936245] or (Mattick et al., WO 2009/124341), or (Corey et al., US 2010/0273863) [sequences B936246-B936265], or (Wahlstedt et al., US 2009/0258925) [sequences B935060-B935126], or BACE: US 2009/0258925 [sequences B935060-B935126]; ApoA1: US 2010/0105760/EP235283 [sequences B935127-B935299], P73, p53, PTEN, WO 2010/065787 A2/EP2370582 [sequences B935300-B935345]; SIRT1: WO 2010/065662 A2/EP09831068 [sequences B935346-B935392]; VEGF: WO 2010/065671-A2/EP2370581-[sequences B935393-B935403]; EPO: WO 2010/065792 A2/EP09831152 [sequences B935404-B935412]; BDNF: WO2010/093904 [sequences B935413-B935423], DLK1: WO 2010/107740 [sequences B935424-B935430]; NRF2/NFE2L2: WO 2010/107733 [sequences B935431-B935438]; GDNF: WO 2010/093906 [sequences B935439-B935476]; SOX2, KLF4, Oct3A/B, “reprogramming factors: WO 2010/135329 [sequences B935477-B935493]; Dystrophin: WO 2010/129861-[sequences B935494-B935525]; ABCA1, LCAT, LRP1, ApoE, LDLR, ApoA1: WO 2010/129799 [sequences B935526-B935804]; HgF: WO 2010/127195 [sequences B935805-B935809]; TTP/Zfp36: WO 2010/129746[sequences B935810-B935824]; TFE3, IRS2: WO 2010/135695 [sequences B935825-B935839]; RIG1, MDA5, IFNA1: WO 2010/138806 [sequences B935840-B935878]; PON1: WO 2010/148065 [sequences B935879-B935885]; Collagen: WO/2010/148050 [sequences B935886-B935918]; Dyrk1A, Dscr1, “Down Syndrome Gene”: WO/2010/151674 [sequences B935919-B935942]; TNFR2: WO/2010/151671-[sequences B935943-B935951]; Insulin: WO/2011/017516 [sequences B935952-B935963]; ADIPOQ: WO/2011/019815 [sequences B935964-B935992]; CHIP: WO/2011/022606 [sequences B935993-B936004]; ABCB1: WO/2011/025862 [sequences B936005-B936014]; NEUROD1, EUROD1, HNF4A, MAFA, PDX, KX6, “Pancreatic development gene”: WO/2011/085066 [sequences B936015-B936054]; MBTPS1: WO/2011/084455 [sequences B936055-B936059]; SHBG: WO/2011/085347 [sequences B936060-B936075]; IRF8: WO/2011/082409 [sequences B936076-B936080]; UCP2: WO/2011/079263 [sequences B936081-B936093]; HGF: WO/2011/079261-[sequences B936094-B936104]; GH: WO/2011/038205 [sequences B936105-B936110]; IQGAP: WO/2011/031482 [sequences B936111-B936116]; NRF1: WO/2011/090740 [sequences B936117-B936123]; P63: WO/2011/090741-[sequences B936124-B936128]; RNAseH1: WO/2011/091390 [sequences B936129-B936140]; ALOX12B: WO/2011/097582 [sequences B936141-B936146]; PYCR1: WO/2011/103528 [sequences B936147-B936151]; CSF3: WO/2011/123745 [sequences B936152-B936157]; FGF21: WO/2011/127337 [sequences B936158-B936165]; SIRTUIN (SIRT): WO2011/139387 [sequences B936266-B936369 and B936408-B936425]; PAR4: WO2011/143640 [sequences B936370-B936376 and B936426]; LHX2: WO2011/146675 [sequences B936377-B936388 and B936427 B936429]; BCL2L11: WO2011/146674 [sequences B936389-B936398 and B936430 B936431]; MSRA: WO2011/150007 [sequences B936399-B936405 and B936432]; ATOH1: WO2011/150005 [sequences B936406-B936407 and B936433] of which each of the foregoing is incorporated by reference in its entirety herein. In some or any of the embodiments, optionally excluded from the invention are of oligonucleotides that specifically bind to, or are complementary to, any one or more of the following regions: Nucleotides 1-932 of sequence B935128; Nucleotides 1-1675 of sequence B935306; Nucleotides 1-518 of sequence B935307; Nucleotides 1-759 of sequence B935308; Nucleotides 1-25892 of sequence B935309; Nucleotides 1-279 of sequence B935310; Nucleotides 1-1982 of sequence B935311; Nucleotides 1-789 of sequence B935312; Nucleotides 1-467 of sequence B935313; Nucleotides 1-1028 of sequence B935347; Nucleotides 1-429 of sequence B935348; Nucleotides 1-156 of sequence B935349; Nucleotides 1-593 of sequence B935350; Nucleotides 1-643 of sequence B935395; Nucleotides 1-513 of sequence B935396; Nucleotides 1-156 of sequence B935406; Nucleotides 1-3175 of sequence B935414; Nucleotides 1-1347 of sequence B935426; Nucleotides 1-5808 of sequence B935433; Nucleotides 1-237 of sequence B935440; Nucleotides 1-1246 of sequence B935441; Nucleotides 1-684 of sequence B935442; Nucleotides 1-400 of sequence B935473; Nucleotides 1-619 of sequence B935474; Nucleotides 1-813 of sequence B935475; Nucleotides 1-993 of sequence B935480; Nucleotides 1-401 of sequence B935480; Nucleotides 1-493 of sequence B935481; Nucleotides 1-418 of sequence B935482; Nucleotides 1-378 of sequence B935496; Nucleotides 1-294 of sequence B935497; Nucleotides 1-686 of sequence B935498; Nucleotides 1-480 of sequence B935499; Nucleotides 1-501 of sequence B935500; Nucleotides 1-1299 of sequence B935533; Nucleotides 1-918 of sequence B935534; Nucleotides 1-1550 of sequence B935535; Nucleotides 1-329 of sequence B935536; Nucleotides 1-1826 of sequence B935537; Nucleotides 1-536 of sequence B935538; Nucleotides 1-551 of sequence B935539; Nucleotides 1-672 of sequence B935540; Nucleotides 1-616 of sequence B935541; Nucleotides 1-471 of sequence B935542; Nucleotides 1-707 of sequence B935543; Nucleotides 1-741 of sequence B935544; Nucleotides 1-346 of sequence B935545; Nucleotides 1-867 of sequence B935546; Nucleotides 1-563 of sequence B935547; Nucleotides 1-970 of sequence B935812; Nucleotides 1-1117 of sequence B935913; Nucleotides 1-297 of sequence B935814; Nucleotides 1-497 of sequence B935827; Nucleotides 1-1267 of sequence B935843; Nucleotides 1-586 of sequence B935844; Nucleotides 1-741 of sequence B935845; Nucleotides 1-251 of sequence B935846; Nucleotides 1-681 of sequence B935847; Nucleotides 1-580 of sequence B935848; Nucleotides 1-534 of sequence B935880; Nucleotides 1-387 of sequence B935889; Nucleotides 1-561 of sequence B935890; Nucleotides 1-335 of sequence B935891; Nucleotides 1-613 of sequence B935892; Nucleotides 1-177 of sequence B935893; Nucleotides 1-285 of sequence B935894; Nucleotides 1-3814 of sequence B935921; Nucleotides 1-633 of sequence B935922; Nucleotides 1-497 of sequence B935923 Nucleotides 1-545 of sequence B935924; Nucleotides 1-413 of sequence B935950; Nucleotides 1-413 of sequence B935951; Nucleotides 1-334 of sequence B935962; Nucleotides 1-582 of sequence B935963; Nucleotides 1-416 of sequence B935964; Nucleotides 1-3591 of sequence B935990; Nucleotides 1-875 of sequence B935991; Nucleotides 1-194 of sequence B935992; Nucleotides 1-2074 of sequence B936003; Nucleotides 1-1237 of sequence B936004; Nucleotides 1-4050 of sequence B936013; Nucleotides 1-1334 of sequence B936014; Nucleotides 1-1235 of sequence B936048; Nucleotides 1-17,964 of sequence B936049; Nucleotides 1-50,003 of sequence B936050; Nucleotides 1-486 of sequence B936051; Nucleotides 1-494 of sequence B936052; Nucleotides 1-1992 of sequence B936053; Nucleotides 1-1767 of sequence B936054; Nucleotides 1-1240 of sequence B936059; Nucleotides 1-3016 of sequence B936074; Nucleotides 1-1609 of sequence B936075; Nucleotides 1-312 of sequence B936080; Nucleotides 1-243 of sequence B936092; Nucleotides 1-802 of sequence B936093; Nucleotides 1-514 of sequence B936102; Nucleotides 1-936 of sequence B936103; Nucleotides 1-1075 of sequence B936104; Nucleotides 1-823 of sequence B936110; Nucleotides 1-979 of sequence B936116; Nucleotides 1-979 of sequence B936123; Nucleotides 1-288 of sequence B936128; Nucleotides 1-437 of sequence B936137; Nucleotides 1-278 of sequence B936138; Nucleotides 1-436 of sequence B936139; Nucleotides 1-1140 of sequence B936140; Nucleotides 1-2082 of sequence B936146; Nucleotides 1-380 of sequence B936151; Nucleotides 1-742 of sequence B936157; Nucleotides 1-4246 of sequence B936165; Nucleotides 1-1028 of sequence B936408; Nucleotides 1-429 of sequence B936409; Nucleotides 1-508 of sequence B936410; Nucleotides 1-593 of sequence B936411; Nucleotides 1-373 of sequence B936412; Nucleotides 1-1713 of sequence B936413; Nucleotides 1-660 of sequence B936414; Nucleotides 1-589 of sequence B936415; Nucleotides 1-726 of sequence B936416; Nucleotides 1-320 of sequence B936417; Nucleotides 1-616 of sequence B936418; Nucleotides 1-492 of sequence B936419; Nucleotides 1-428 of sequence B936420; Nucleotides 1-4041 of sequence B936421; Nucleotides 1-705 of sequence B936422; Nucleotides 1-2714 of sequence B936423; Nucleotides 1-1757 of sequence B936424; Nucleotides 1-3647 of sequence B936425; Nucleotides 1-354 of sequence B936426; Nucleotides 1-2145 of sequence B936427, Nucleotides 1-606 of sequence B936428; Nucleotides 1-480 of sequence B936429; Nucleotides 1-3026 of sequence B936430; Nucleotides 1-1512 of sequence B936431; Nucleotides 1-3774 of sequence B936432; and Nucleotides 1-589 of sequence B936433. In some or any of the embodiments of the oligonucleotides described herein, or processes for designing or synthesizing them, the oligonucleotides will upregulate gene expression and may specifically bind or specifically hybridize or be complementary to the PRC2 binding RNA that is transcribed from the same strand as a protein coding reference gene. The oligonucleotide may bind to a region of the PRC2 binding RNA that originates within or overlaps an intron, exon, intron exon junction, 5′ UTR, 3′ UTR, a translation initiation region, or a translation termination region of a protein coding sense strand of a reference gene (refGene).

In some or any of the embodiments of oligonucleotides described herein, or processes for designing or synthesizing them, the oligonucleotides will upregulate gene expression and may specifically bind or specifically hybridize or be complementary to a PRC2 binding RNA that transcribed from the opposite strand (the antisense strand) of a protein coding reference gene. The oligonucleotide may bind to a region of the PRC2 binding RNA that originates within or overlaps an intron, exon, intron exon junction, 5′ UTR, 3′ UTR, a translation initiation region, or a translation termination region of a protein coding antisense strand of a reference gene

The oligonucleotides described herein may be modified, e.g., comprise a modified sugar moiety, a modified internucleoside linkage, a modified nucleotide and/or combinations thereof. In addition, the oligonucleotides can exhibit one or more of the following properties: do not induce substantial cleavage or degradation of the target RNA; do not cause substantially complete cleavage or degradation of the target RNA; do not activate the RNAse H pathway; do not activate RISC; do not recruit any Argonaute family protein; are not cleaved by Dicer; do not mediate alternative splicing; are not immune stimulatory; are nuclease resistant; have improved cell uptake compared to unmodified oligonucleotides; are not toxic to cells or mammals; may have improved endosomal exit; do interfere with interaction of lncRNA with PRC2, preferably the Ezh2 subunit but optionally the Suz12, Eed, RbAp46/48 subunits or accessory factors such as Jarid2; do decrease histone H3 lysine27 methylation and/or do upregulate gene expression.

In some or any of the embodiments of oligonucleotides described herein, or processes for designing or synthesizing them, the oligonucleotides may optionally exclude those that bind DNA of a promoter region, as described in Kuwabara et al., US 2005/0226848 or Li et al., US 2010/0210707 or Corey et al., U.S. Pat. No. 7,709,456 or Mattick et al., WO 2009/124341, or those that bind DNA of a 3′ UTR region, as described in Corey et al., US 2010/0273863.

Oligonucleotides that are designed to interact with RNA to modulate gene expression are a distinct subset of base sequences from those that are designed to bind a DNA target (e.g., are complementary to the underlying genomic DNA sequence from which the RNA is transcribed).

Methods for Modulating Gene Expression

In another aspect, the invention relates to methods for modulating gene expression in a cell, e.g., a cancer cell, a stem cell, or other normal cell types for gene or epigenetic therapy. The cells can be in vitro, ex vivo, or in vivo (e.g., in a subject who has cancer, e.g., a tumor). In some embodiments, methods for modulating gene expression in a cell comprise delivering a single stranded oligonucleotide as described herein. In some embodiments, delivery of the single stranded oligonucleotide to the cell results in a level of expression of gene that is at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more greater than a level of expression of gene in a control cell to which the single stranded oligonucleotide has not been delivered. In certain embodiments, delivery of the single stranded oligonucleotide to the cell results in a level of expression of gene that is at least 50% greater than a level of expression of gene in a control cell to which the single stranded oligonucleotide has not been delivered.

In another aspect of the invention, methods comprise administering to a subject (e.g. a human) a composition comprising a single stranded oligonucleotide as described herein to increase protein levels in the subject. In some embodiments, the increase in protein levels is at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, or more, higher than the amount of a protein in the subject before administering.

As another example, to increase expression of a tumor suppressor in a cell, the methods include introducing into the cell a single stranded oligonucleotide that is sufficiently complementary to a PRC2-associated region (e.g., of a long non-coding RNA) that maps to a genomic position encompassing or in proximity to a target gene (e.g., a tumor suppressor as set forth in Table 2 of International Patent Application Publication WO/2012/087983, an imprinted gene in Table 2, and/or other growth-suppressing genes in Table 2 of International Patent Application Publication WO/2012/087983 (e.g., Nkx2-1 or Titf-1, e.g., in subjects with cancer, e.g., lung adenocarcinoma patients)).

In another aspect of the invention provides methods of treating a condition (e.g., cancer) associated with decreased levels of expression of a particular gene in a subject, the method comprising administering a single stranded oligonucleotide as described herein.

A subject can include a non-human mammal, e.g. mouse, rat, guinea pig, rabbit, cat, dog, goat, cow, or horse. In preferred embodiments, a subject is a human.

In some embodiments, specific cancers that can be treated using the methods described herein are listed in Table 3 of International Patent Application Publication WO/2012/087983, for example, and include, but are not limited to: breast, lung, prostate, CNS (e.g., glioma), salivary gland, prostate, ovarian, and leukemias (e.g., ALL, CML, or AML). Associations of these genes with a particular cancer are known in the art, e.g., as described in Futreal et al., Nat Rev Cancer. 2004; 4; 177-83 (see, e.g., Table 1, incorporated by reference herein); and The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website, Bamford et al., Br J Cancer. 2004; 91; 355-8; see also Forbes et al., Curr Protoc Hum Genet. 2008; Chapter 10; Unit 10.11, and the COSMIC database, e.g., v. 50 (Nov. 30, 2010). It is understood that reference to any particular type of cancer in, for example, Table 3 of International Patent Application Publication WO/2012/087983, means that patients with other types of cancer, i.e., cancer in general, may be treated.

In addition, the methods described herein can be used for modulating (e.g., enhancing or decreasing) pluripotency of a stem cell and to direct stem cells down specific differentiation pathways to make endoderm, mesoderm, ectoderm, and their developmental derivatives. To increase, maintain, or enhance pluripotency, the methods include introducing into the cell a single stranded oligonucleotide that specifically binds to, or is complementary to, a PRC2-associated region of a nucleic acid (e.g., of any long non-coding RNA disclosed herein). Stem cells useful in the methods described herein include adult stem cells (e.g., adult stem cells obtained from the inner ear, bone marrow, mesenchyme, skin, fat, liver, muscle, or blood of a subject, e.g., the subject to be treated); embryonic stem cells, or stem cells obtained from a placenta or umbilical cord; progenitor cells (e.g., progenitor cells derived from the inner ear, bone marrow, mesenchyme, skin, fat, liver, muscle, or blood); and induced pluripotent stem cells (e.g., iPS cells).

In some embodiments, the methods described herein include administering a composition, e.g., a sterile composition, comprising a single stranded oligonucleotide that is complementary to a PRC2-associated region of a nucleic acid (e.g., of an lncRNA described herein, e.g., as set forth in sequences A1 to A193,049, B1 to B916,209, and B916,626 to B934,931). In some embodiments, the single stranded oligonucleotide comprises one or more modified nucleotides (e.g., a locked nucleic acid (LNA) molecule).

Single stranded oligonucleotides have been employed as therapeutic moieties in the treatment of disease states in animals, including humans. Single stranded oligonucleotides can be useful therapeutic modalities that can be configured to be useful in treatment regimes for the treatment of cells, tissues and animals, especially humans.

For therapeutics, an animal, preferably a human, suspected of having cancer is treated by administering single stranded oligonucleotide in accordance with this invention. For example, in one non-limiting embodiment, the methods comprise the step of administering to the animal in need of treatment, a therapeutically effective amount of a single stranded oligonucleotide as described herein.

Formulation, Delivery, And Dosing

The oligonucleotides described herein can be formulated for administration to a subject. It should be understood that the formulations, compositions and methods can be practiced with any of the oligonucleotides disclosed herein.

The formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. The amount of active ingredient (e.g., an oligonucleotide or compound of the invention) which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, the particular mode of administration, e.g., intradermal or inhalation. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound which produces a therapeutic effect, e.g. tumor regression.

Pharmaceutical formulations of this invention can be prepared according to any method known to the art for the manufacture of pharmaceuticals. Such formulations can contain sweetening agents, flavoring agents, coloring agents and preserving agents. A formulation can be admixtured with nontoxic pharmaceutically acceptable excipients which are suitable for manufacture. Formulations may comprise one or more diluents, emulsifiers, preservatives, buffers, excipients, etc. and may be provided in such forms as liquids, powders, emulsions, lyophilized powders, sprays, creams, lotions, controlled release formulations, tablets, pills, gels, on patches, in implants, etc.

A formulated single stranded oligonucleotide composition can assume a variety of states. In some examples, the composition is at least partially crystalline, uniformly crystalline, and/or anhydrous (e.g., less than 80, 50, 30, 20, or 10% water). In another example, the single stranded oligonucleotide is in an aqueous phase, e.g., in a solution that includes water. The aqueous phase or the crystalline compositions can, e.g., be incorporated into a delivery vehicle, e.g., a liposome (particularly for the aqueous phase) or a particle (e.g., a microparticle as can be appropriate for a crystalline composition). Generally, the single stranded oligonucleotide composition is formulated in a manner that is compatible with the intended method of administration.

In some embodiments, the composition is prepared by at least one of the following methods: spray drying, lyophilization, vacuum drying, evaporation, fluid bed drying, or a combination of these techniques; or sonication with a lipid, freeze-drying, condensation and other self-assembly.

A single stranded oligonucleotide preparation can be formulated or administered (together or separately) in combination with another agent, e.g., another therapeutic agent or an agent that stabilizes a single stranded oligonucleotide, e.g., a protein that complexes with single stranded oligonucleotide. Still other agents include chelators, e.g., EDTA (e.g., to remove divalent cations such as Mg²⁺), salts, RNAse inhibitors (e.g., a broad specificity RNAse inhibitor such as RNAsin) and so forth.

In one embodiment, the single stranded oligonucleotide preparation includes another single stranded oligonucleotide, e.g., a second single stranded oligonucleotide that modulates expression of a second gene or a second single stranded oligonucleotide that modulates expression of the first gene. Still other preparation can include at least 3, 5, ten, twenty, fifty, or a hundred or more different single stranded oligonucleotide species. Such single stranded oligonucleotides can mediated gene expression with respect to a similar number of different genes.

In one embodiment, the single stranded oligonucleotide preparation includes at least a second therapeutic agent (e.g., an agent other than an oligonucleotide). For example, e.g., a single stranded oligonucleotide composition for the treatment of a cancer might further comprise a chemotherapeutic agent.

Route of Delivery

A composition that includes a single stranded oligonucleotide can be delivered to a subject by a variety of routes. Exemplary routes include: intravenous, intradermal, topical, rectal, parenteral, anal, intravaginal, intranasal, pulmonary, ocular.

The single stranded oligonucleotide molecules of the invention can be incorporated into pharmaceutical compositions suitable for administration. Such compositions typically include one or more species of single stranded oligonucleotide and a pharmaceutically acceptable carrier. As used herein the language “pharmaceutically acceptable carrier” is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.

The pharmaceutical compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic, vaginal, rectal, intranasal, transdermal), oral or parenteral. Parenteral administration includes intravenous drip, subcutaneous, intraperitoneal or intramuscular injection, or intrathecal or intraventricular administration.

The route and site of administration may be chosen to enhance targeting. For example, to target muscle cells, intramuscular injection into the muscles of interest would be a logical choice. Lung cells might be targeted by administering the single stranded oligonucleotide in aerosol form. The vascular endothelial cells could be targeted by coating a balloon catheter with the single stranded oligonucleotide and mechanically introducing the oligonucleotide.

Topical Delivery

Topical administration refers to the delivery to a subject by contacting the formulation directly to a surface of the subject. The most common form of topical delivery is to the skin, but a composition disclosed herein can also be directly applied to other surfaces of the body, e.g., to the eye, a mucous membrane, to surfaces of a body cavity or to an internal surface. As mentioned above, the most common topical delivery is to the skin. The term encompasses several routes of administration including, but not limited to, topical and transdermal. These modes of administration typically include penetration of the skin's permeability barrier and efficient delivery to the target tissue or stratum. Topical administration can be used as a means to penetrate the epidermis and dermis and ultimately achieve systemic delivery of the composition. Topical administration can also be used as a means to selectively deliver oligonucleotides to the epidermis or dermis of a subject, or to specific strata thereof, or to an underlying tissue.

Formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable. Coated condoms, gloves and the like may also be useful.

Transdermal delivery is a valuable route for the administration of lipid soluble therapeutics. The dermis is more permeable than the epidermis and therefore absorption is much more rapid through abraded, burned or denuded skin. Inflammation and other physiologic conditions that increase blood flow to the skin also enhance transdermal adsorption. Absorption via this route may be enhanced by the use of an oily vehicle (inunction) or through the use of one or more penetration enhancers. Other effective ways to deliver a composition disclosed herein via the transdermal route include hydration of the skin and the use of controlled release topical patches. The transdermal route provides a potentially effective means to deliver a composition disclosed herein for systemic and/or local therapy. In addition, iontophoresis (transfer of ionic solutes through biological membranes under the influence of an electric field), phonophoresis or sonophoresis (use of ultrasound to enhance the absorption of various therapeutic agents across biological membranes, notably the skin and the cornea), and optimization of vehicle characteristics relative to dose position and retention at the site of administration may be useful methods for enhancing the transport of topically applied compositions across skin and mucosal sites.

Oral or Nasal Delivery

Both the oral and nasal membranes offer advantages over other routes of administration. For example, oligonucleotides administered through these membranes may have a rapid onset of action, provide therapeutic plasma levels, avoid first pass effect of hepatic metabolism, and avoid exposure of the oligonucleotides to the hostile gastrointestinal (GI) environment. Additional advantages include easy access to the membrane sites so that the oligonucleotide can be applied, localized and removed easily.

In oral delivery, compositions can be targeted to a surface of the oral cavity, e.g., to sublingual mucosa which includes the membrane of ventral surface of the tongue and the floor of the mouth or the buccal mucosa which constitutes the lining of the cheek. The sublingual mucosa is relatively permeable thus giving rapid absorption and acceptable bioavailability of many agents. Further, the sublingual mucosa is convenient, acceptable and easily accessible.

A pharmaceutical composition of single stranded oligonucleotide may also be administered to the buccal cavity of a human being by spraying into the cavity, without inhalation, from a metered dose spray dispenser, a mixed micellar pharmaceutical formulation as described above and a propellant. In one embodiment, the dispenser is first shaken prior to spraying the pharmaceutical formulation and propellant into the buccal cavity.

Compositions for oral administration include powders or granules, suspensions or solutions in water, syrups, slurries, emulsions, elixirs or non-aqueous media, tablets, capsules, lozenges, or troches. In the case of tablets, carriers that can be used include lactose, sodium citrate and salts of phosphoric acid. Various disintegrants such as starch, and lubricating agents such as magnesium stearate, sodium lauryl sulfate and talc, are commonly used in tablets. For oral administration in capsule form, useful diluents are lactose and high molecular weight polyethylene glycols. When aqueous suspensions are required for oral use, the nucleic acid compositions can be combined with emulsifying and suspending agents. If desired, certain sweetening and/or flavoring agents can be added.

Parenteral Delivery

Parenteral administration includes intravenous drip, subcutaneous, intraperitoneal or intramuscular injection, intrathecal or intraventricular administration. In some embodiments, parental administration involves administration directly to the site of disease (e.g. injection into a tumor).

Formulations for parenteral administration may include sterile aqueous solutions which may also contain buffers, diluents and other suitable additives. Intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir. For intravenous use, the total concentration of solutes should be controlled to render the preparation isotonic.

Ocular Delivery

Any of the single stranded oligonucleotides described herein can be administered to ocular tissue. For example, the compositions can be applied to the surface of the eye or nearby tissue, e.g., the inside of the eyelid. For ocular administration, ointments or droppable liquids may be delivered by ocular delivery systems known to the art such as applicators or eye droppers. Such compositions can include mucomimetics such as hyaluronic acid, chondroitin sulfate, hydroxypropyl methylcellulose or poly(vinyl alcohol), preservatives such as sorbic acid, EDTA or benzylchronium chloride, and the usual quantities of diluents and/or carriers. The single stranded oligonucleotide can also be administered to the interior of the eye, and can be introduced by a needle or other delivery device which can introduce it to a selected area or structure.

Pulmonary Delivery

Pulmonary delivery compositions can be delivered by inhalation by the patient of a dispersion so that the composition, preferably single stranded oligonucleotides, within the dispersion can reach the lung where it can be readily absorbed through the alveolar region directly into blood circulation. Pulmonary delivery can be effective both for systemic delivery and for localized delivery to treat diseases of the lungs.

Pulmonary delivery can be achieved by different approaches, including the use of nebulized, aerosolized, micellular and dry powder-based formulations. Delivery can be achieved with liquid nebulizers, aerosol-based inhalers, and dry powder dispersion devices. Metered-dose devices are preferred. One of the benefits of using an atomizer or inhaler is that the potential for contamination is minimized because the devices are self-contained. Dry powder dispersion devices, for example, deliver agents that may be readily formulated as dry powders. A single stranded oligonucleotide composition may be stably stored as lyophilized or spray-dried powders by itself or in combination with suitable powder carriers. The delivery of a composition for inhalation can be mediated by a dosing timing element which can include a timer, a dose counter, time measuring device, or a time indicator which when incorporated into the device enables dose tracking, compliance monitoring, and/or dose triggering to a patient during administration of the aerosol medicament.

The term “powder” means a composition that consists of finely dispersed solid particles that are free flowing and capable of being readily dispersed in an inhalation device and subsequently inhaled by a subject so that the particles reach the lungs to permit penetration into the alveoli. Thus, the powder is said to be “respirable.” Preferably the average particle size is less than about 10 μm in diameter preferably with a relatively uniform spheroidal shape distribution. More preferably the diameter is less than about 7.5 μm and most preferably less than about 5.0 μm. Usually the particle size distribution is between about 0.1 μm and about 5 μm in diameter, particularly about 0.3 μm to about 5 μm.

The term “dry” means that the composition has a moisture content below about 10% by weight (% w) water, usually below about 5% w and preferably less it than about 3% w. A dry composition can be such that the particles are readily dispersible in an inhalation device to form an aerosol.

The term “therapeutically effective amount” is the amount of oligonucleotide present in the composition that is needed to provide the desired level of target gene expression in the subject to be treated to give the anticipated physiological response. The term “physiologically effective amount” is that amount delivered to a subject to give the desired palliative or curative effect. The term “pharmaceutically acceptable carrier” means that the carrier can be taken into the lungs with no significant adverse toxicological effects on the lungs.

The types of pharmaceutical excipients that are useful as carrier include stabilizers such as human serum albumin (HSA), bulking agents such as carbohydrates, amino acids and polypeptides; pH adjusters or buffers; salts such as sodium chloride; and the like. These carriers may be in a crystalline or amorphous form or may be a mixture of the two.

Suitable pH adjusters or buffers include organic salts prepared from organic acids and bases, such as sodium citrate, sodium ascorbate, and the like; sodium citrate is preferred. Pulmonary administration of a micellar single stranded oligonucleotide formulation may be achieved through metered dose spray devices with propellants such as tetrafluoroethane, heptafluoroethane, dimethylfluoropropane, tetrafluoropropane, butane, isobutane, dimethyl ether and other non-CFC and CFC propellants.

Devices and Implants

Exemplary devices include devices which are introduced into the vasculature, e.g., devices inserted into the lumen of a vascular tissue, or which devices themselves form a part of the vasculature, including stents, catheters, heart valves, and other vascular devices. These devices, e.g., catheters or stents, can be placed in the vasculature of the lung, heart, or leg.

Other devices include non-vascular devices, e.g., devices implanted in the peritoneum, or in organ or glandular tissue, e.g., artificial organs. The device can release a therapeutic substance in addition to a single stranded oligonucleotide, e.g., a device can release insulin.

In one embodiment, unit doses or measured doses of a composition that includes single stranded oligonucleotide are dispensed by an implanted device. The device can include a sensor that monitors a parameter within a subject. For example, the device can include pump, e.g., and, optionally, associated electronics.

Tissue, e.g., cells or organs can be treated with a single stranded oligonucleotide, ex vivo and then administered or implanted in a subject. The tissue can be autologous, allogeneic, or xenogeneic tissue. E.g., tissue can be treated to reduce graft v. host disease. In other embodiments, the tissue is allogeneic and the tissue is treated to treat a disorder characterized by unwanted gene expression in that tissue. E.g., tissue, e.g., hematopoietic cells, e.g., bone marrow hematopoietic cells, can be treated to inhibit unwanted cell proliferation. Introduction of treated tissue, whether autologous or transplant, can be combined with other therapies. In some implementations, the single stranded oligonucleotide treated cells are insulated from other cells, e.g., by a semi-permeable porous barrier that prevents the cells from leaving the implant, but enables molecules from the body to reach the cells and molecules produced by the cells to enter the body. In one embodiment, the porous barrier is formed from alginate.

In one embodiment, a contraceptive device is coated with or contains a single stranded oligonucleotide. Exemplary devices include condoms, diaphragms, IUD (implantable uterine devices, sponges, vaginal sheaths, and birth control devices.

Dosage

In one aspect, the invention features a method of administering a single stranded oligonucleotide (e.g., as a compound or as a component of a composition) to a subject (e.g., a human subject). In one embodiment, the unit dose is between about 10 mg and 25 mg per kg of bodyweight. In one embodiment, the unit dose is between about 1 mg and 100 mg per kg of bodyweight. In one embodiment, the unit dose is between about 0.1 mg and 500 mg per kg of bodyweight. In some embodiments, the unit dose is more than 0.001, 0.005, 0.01, 0.05, 0.1, 0.5, 1, 2, 5, 10, 25, 50 or 100 mg per kg of bodyweight.

The defined amount can be an amount effective to treat or prevent a disease or disorder, e.g., a disease or disorder associated with the target gene. The unit dose, for example, can be administered by injection (e.g., intravenous or intramuscular), an inhaled dose, or a topical application.

In some embodiments, the unit dose is administered daily. In some embodiments, less frequently than once a day, e.g., less than every 2, 4, 8 or 30 days. In another embodiment, the unit dose is not administered with a frequency (e.g., not a regular frequency). For example, the unit dose may be administered a single time. In some embodiments, the unit dose is administered more than once a day, e.g., once an hour, two hours, four hours, eight hours, twelve hours, etc.

In one embodiment, a subject is administered an initial dose and one or more maintenance doses of a single stranded oligonucleotide. The maintenance dose or doses are generally lower than the initial dose, e.g., one-half less of the initial dose. A maintenance regimen can include treating the subject with a dose or doses ranging from 0.0001 to 100 mg/kg of body weight per day, e.g., 100, 10, 1, 0.1, 0.01, 0.001, or 0.0001 mg per kg of bodyweight per day. The maintenance doses may be administered no more than once every 1, 5, 10, or 30 days. Further, the treatment regimen may last for a period of time which will vary depending upon the nature of the particular disease, its severity and the overall condition of the patient. In some embodiments the dosage may be delivered no more than once per day, e.g., no more than once per 24, 36, 48, or more hours, e.g., no more than once for every 5 or 8 days. Following treatment, the patient can be monitored for changes in his condition and for alleviation of the symptoms of the disease state. The dosage of the oligonucleotide may either be increased in the event the patient does not respond significantly to current dosage levels, or the dose may be decreased if an alleviation of the symptoms of the disease state is observed, if the disease state has been ablated, or if undesired side-effects are observed.

The effective dose can be administered in a single dose or in two or more doses, as desired or considered appropriate under the specific circumstances. If desired to facilitate repeated or frequent infusions, implantation of a delivery device, e.g., a pump, semi-permanent stent (e.g., intravenous, intraperitoneal, intracisternal or intracapsular), or reservoir may be advisable.

In some embodiments, the oligonucleotide pharmaceutical composition includes a plurality of single stranded oligonucleotide species. In another embodiment, the single stranded oligonucleotide species has sequences that are non-overlapping and non-adjacent to another species with respect to a naturally occurring target sequence (e.g., a PRC2-associated region). In another embodiment, the plurality of single stranded oligonucleotide species is specific for different PRC2-associated regions. In another embodiment, the single stranded oligonucleotide is allele specific.

In some cases, a patient is treated with a single stranded oligonucleotide in conjunction with other therapeutic modalities. For example, a patient being treated for cancer may be administered a single stranded oligonucleotide in conjunction with a chemotherapy.

Following successful treatment, it may be desirable to have the patient undergo maintenance therapy to prevent the recurrence of the disease state, wherein the compound of the invention is administered in maintenance doses, ranging from 0.0001 mg to 100 mg per kg of body weight.

The concentration of the single stranded oligonucleotide composition is an amount sufficient to be effective in treating or preventing a disorder or to regulate a physiological condition in humans. The concentration or amount of single stranded oligonucleotide administered will depend on the parameters determined for the agent and the method of administration, e.g. nasal, buccal, pulmonary. For example, nasal formulations may tend to require much lower concentrations of some ingredients in order to avoid irritation or burning of the nasal passages. It is sometimes desirable to dilute an oral formulation up to 10-100 times in order to provide a suitable nasal formulation.

Certain factors may influence the dosage required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general health and/or age of the subject, and other diseases present. Moreover, treatment of a subject with a therapeutically effective amount of a single stranded oligonucleotide can include a single treatment or, preferably, can include a series of treatments. It will also be appreciated that the effective dosage of a single stranded oligonucleotide used for treatment may increase or decrease over the course of a particular treatment. For example, the subject can be monitored after administering a single stranded oligonucleotide composition. Based on information from the monitoring, an additional amount of the single stranded oligonucleotide composition can be administered.

Dosing is dependent on severity and responsiveness of the disease condition to be treated, with the course of treatment lasting from several days to several months, or until a cure is effected or a diminution of disease state is achieved. Optimal dosing schedules can be calculated from measurements of target gene expression levels in the body of the patient. Persons of ordinary skill can easily determine optimum dosages, dosing methodologies and repetition rates. Optimum dosages may vary depending on the relative potency of individual compounds, and can generally be estimated based on EC50s found to be effective in in vitro and in vivo animal models. In some embodiments, the animal models include transgenic animals that express a human target gene. In another embodiment, the composition for testing includes a single stranded oligonucleotide that is complementary, at least in an internal region, to a sequence that is conserved between the target gene in the animal model and the target gene in a human.

In one embodiment, the administration of the single stranded oligonucleotide composition is parenteral, e.g. intravenous (e.g., as a bolus or as a diffusible infusion), intradermal, intraperitoneal, intramuscular, intrathecal, intraventricular, intracranial, subcutaneous, transmucosal, buccal, sublingual, endoscopic, rectal, oral, vaginal, topical, pulmonary, intranasal, urethral or ocular. Administration can be provided by the subject or by another person, e.g., a health care provider. The composition can be provided in measured doses or in a dispenser which delivers a metered dose. Selected modes of delivery are discussed in more detail below.

Kits

In certain aspects of the invention, kits are provided, comprising a container housing a composition comprising a single stranded oligonucleotide. In some embodiments, the composition is a pharmaceutical composition comprising a single stranded oligonucleotide and a pharmaceutically acceptable carrier. In some embodiments, the individual components of the pharmaceutical composition may be provided in one container. Alternatively, it may be desirable to provide the components of the pharmaceutical composition separately in two or more containers, e.g., one container for single stranded oligonucleotides, and at least another for a carrier compound. The kit may be packaged in a number of different configurations such as one or more containers in a single box. The different components can be combined, e.g., according to instructions provided with the kit. The components can be combined according to a method described herein, e.g., to prepare and administer a pharmaceutical composition. The kit can also include a delivery device.

The present invention is further illustrated by the following Examples, which in no way should be construed as further limiting. The entire contents of all of the references (including literature references, issued patents, published patent applications, and co-pending patent applications) cited throughout this application are hereby expressly incorporated by reference.

EXAMPLES

The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.

Materials and Methods

The following materials and methods were used in the Examples 1-7 set forth below.

RIP-seq

RNA immunoprecipitation was performed using 10⁷ wildtype 16.7 (Lee and Lu, 1999) and Ezh2−/− ES cells. To construct RIP-seq libraries, cell nuclei were isolated, nuclear lysates were prepared, treated with 400 U/ml DNAse, and incubated with anti-Ezh2 antibodies (Active Motif) or control IgG (Cell Signaling Technology). RNA-protein complexes were immunoprecipitated with protein A agarose beads and RNA extracted using Trizol (Invitrogen). To preserve strand information, template switching was used for the library construction. 20-150 ng RNA and Adaptor1 (5′-CTTTCCCTACACGACGCTCTTCCGATCTNNNNNN-3′; SEQ ID NO: 1277) were used for first-strand cDNA synthesis using Superscript II Reverse Transcription Kit (Invitrogen). Superscript II adds non-template CCC 3′ overhangs, which were used to hybridize to Adaptor2-GGG template-switch primer (5′-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCTGGG-3′; SEQ ID NO: 1278). During 1^(st)-strand cDNA synthesis, samples were incubated with adaptor1 at 20° C. for 10 min, followed by 37° C. for 10 min and 42° C. for 45 min. Denatured template switch primer was then added and each tube incubated for 30 min at 42° C., followed by 75° C. for 15 min. Resulting cDNAs were amplified by forward (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGA TCT-3′; SEQ ID NO: 1279) and reverse (5′-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT-3′; SEQ ID NO: 1280) Illumina primers. PCR was performed by Phusion polymerase (BioRad) as follows: 98° C. for 30 s, 20-24 cycles of [98° C. 10 s, 65° C. 30 s, 72° C. 30 s], and 72° C. for 5 min. PCR products were loaded on 3% NuSieve gel for size-selection and 200-1,200 bp products were excised and extracted by QIAEX II Agarose Gel Extraction Kit (Qiagen). Minus-RT samples generally yielded no products. DNA concentrations were quantitated by PicoGreen. 5-10 ml of 2-20 nM cDNA samples were sequenced by the Sequencing Core Facility of the Dept. of Molecular Biology, MGH, on the Illumina GAII.

Bioinformatic Analysis

Except as noted below, all analyses were performed using C++ programs. Image processing and base calling were performed using the Illumina pipeline. 3′ adaptor sequences were detected by crossmatch and matches of ≧5 bases were trimmed, homopolymer reads filtered, and reads matching the mitochondrial genome and ribosomal RNAs excluded from all subsequent analyses. Remaining sequences were then aligned to the mm9 mouse reference genome using shortQueryLookup (Batzoglou et al., 2002). Alignments with ≦1 error were retained. Because library construction and sequencing generate sequence from the opposite strand of the PRC2-bound RNA, in all further analysis, we treated each read as if it were reverse-complemented. To determine the correlation coefficients comparing the original α-Ezh2 RIP-seq library to its technical and biological replicates and also to RIP-seq of the Ezh2−/− control line the number of reads per gene was compared between two samples and, for each pair, the Pearson correlation was computed between the number of reads mapped to each refGene. That is, for each sample, a vector was created of counts of reads mapped to each refGene and computed the Pearson correlation between all pairs of vectors.

Locations of repetitive sequences in mm9 (RepeatMasker) were obtained from the UCSC Genome Browser database. The overlap of PRC2 transcriptome reads with these repeats was obtained by intersecting coordinates of RepeatMasker data with coordinates of read alignments. The UCSC transcriptome was used as general reference. To obtain a set of non-overlapping distinct transcribed regions, the UCSC transcriptome transcripts were sorted by start coordinate and merged overlapping transcripts on the same strand (joined UCSC transcriptome: 39,003 transcripts total). Read alignment coordinates were intersected with those of the merged UCSC transcripts to determine the number of UCSC transcripts present in the PRC2 transcriptome. Hits to the transcripts were converted to RPKM units, where the read count is 1/(n*K*M), and n is the number of alignments in the genome, K is the transcript length divided by 1,000, and M is the sequencing depth including only reads mapping to mm9 divided by 1,000,000. This normalization allows for comparisons between transcripts of differing lengths and between samples of differing sequencing depths.

To generate promoter maps, promoter regions were defined as −10,000 to +2000 bases relative to TSS (obtained from refGene catalog, UCSC Genome Browser). Read counts overlapping promoter regions were plotted, except that the limit of 10 alignments was relaxed. For chromosomal alignments read numbers were computed for all non-overlapping consecutive 100 kb windows on each chromosome. Reads were normalized such that those mapping to n locations were counted as 1/n^(th) of a read at each location. Graphs were plotted using custom scripts written in R. A list of all enriched transcripts were found by comparing the RPKM scores on each strand for all transcripts in the WT and Ezh2−/− samples. Then their coordinates were intersected with coordinates of the feature of interest. Features not in NCBI37/mm9 mouse assembly coordinates were converted to those coordinates using UCSC's LiftOver utility. The liftOver utility effectively maps one genome to another, allowing rapid identification of regions of interest between successive assemblies of the same species or between two distinct species.

RIP/qRT-PCR

Validation RIPs were performed, based on existing methods, using 5 ul of rabbit anti-mouse-Ezh2 antibodies (Active Motif) or normal rabbit IgG (Millipore). RIP was followed by quantitative, strand-specific RT-PCR using the ICYCLER IQ Real-time detection system (BioRad). Gene-specific PCR primer pairs are:

Malat-1: SEQ ID NO: 1281 Forward 5′-GCCTTTTGTCACCTCACT-3′; SEQ ID NO: 1282 Reverse 5′-CAAACTCACTGCAAGGTCTC-3′; Malat1-as: SEQ ID NO: 1283 Forward 5′-TACTGGGTCTGGATTCTCTG-3′; SEQ ID NO: 1284 Reverse 5′-CAGTTCCGTGGTCTTTAGTG-3′; Foxn2-as: SEQ ID NO: 1285 Forward5′-GGCTATGCTCATGCTGTAAC; SEQ ID NO: 1286 Reverse 5′-GTTACTGGCATCTTTCTCACA-3′; Ly6e-as: SEQ ID NO: 1287 Forward 5′-CCACACCGAGATTGAGATTG-3′; SEQ ID NO: 1288 Reverse 5′-GCCAGGAGAAAGACCATTAC-3′; Bgn-as: SEQ ID NO: 1289 Forward 5′-TGTGAACCCTTTCCTGGA-3′; SEQ ID NO: 1290 Reverse 5′-CTTCACAGGTCTCTAGCCA-3′; Gtl2: SEQ ID NO: 1291 Forward 5′-CGAGGACTTCACGCACAAC-3′; SEQ ID NO: 1292 Reverse 5′-TTACAGTTGGAGGGTCCTGG-3′; Gtl2-as: SEQ ID NO: 1293 Forward 5′-CACCCTGAACATCCAACA-3′; SEQ ID NO: 1294 Reverse 5′-CATCTGCTTTTCCTACCTGG-3′; Hapa1-upstream: SEQ ID NO: 1227 Forward 5′-GGTCCAAAATCGGCAGT-3′; SEQ ID NO: 1228 Reverse 5′-GTCCTCAAATCCCTACCAGA-3′; Htr6-downstream: SEQ ID NO: 1229 Forward 5′-ACACGGTCGTGAAGCTAGGTA-3′; SEQ ID NO: 1230 Reverse 5′-CAGTTGGAGTAGGCCATTCCC-3′; Nespas/TR019501: SEQ ID NO: 1231 Forward 5′-AGATGAGTCCAGGTGCTT-3′; SEQ ID NO: 1232 Reverse 5′-CAAGTCCAGAGTAGCCAAC-3′;

Xist-Forward 3F5 and -Reverse 2R primers have been described (Zhao et al., 2008). For strand-specific cDNA synthesis, the reverse primer was used, qPCR carried out with SYBR green (BioRad), and threshold crossings (Ct) recorded. Each value was normalized to input RNA levels.

Northern Blot Analysis

5 μg of poly(A+) RNA were isolated from 16.7 ES cells, separated by 0.8% agarose gel containing formaldehyde, blotted onto Hybond-XL (GE Healthcare), and hybridized to probe using Ultrahyb (Ambion) at 42° C. Probes were generated using STRIP-EZ PCR kit (Ambion) and amplified from genomic DNA with:

Malat1-AS-F, SEQ ID NO: 1233 5′-TGGGCTATTTTTCCTTACTGG-3′; Malat1-AS-R, SEQ ID NO: 1234 5′-GAGTCCCTTTGCTGTGCTG-3′; (Gtl2) Meg3-F, SEQ ID NO: 1235 5′-GCGATAAAGGAAGACACATGC-3′; Meg3-R, SEQ ID NO: 1236 5′-CCACTCCTTACTGGCTGCTC-3′; Meg3 ds-F3, SEQ ID NO: 1237 5′-ATGAAGTCCATGGTGACAGAC-3′; Meg3 ds-R2, SEQ ID NO: 1238 5′-ACGCTCTCGCATACACAATG-3′; Rtl1-F, SEQ ID NO: 1239 5′-GTTGGGGATGAAGATGTCGT-3′; Rtl1-R, SEQ ID NO: 1240 5′-GAGGCACAAGGGAAAATGAC-3′; Nespas ds-F, SEQ ID NO: 1241 5′-TGGACTTGCTACCCAAAAGG-3′; Nespas ds-R, SEQ ID NO: 1242 5′-CGATGTTGCCCAGTTATCAG-3′; Bgn-AS-F, SEQ ID NO: 1243 5′-CAACTGACCTCATAAGCAGCAC-3′; Bgn-AS-R, SEQ ID NO: 1244 5′-AGGCTGCTTTCTGCTTCACA-3′; Htr6 up-F, SEQ ID NO: 1245 5′-ATACTGAAGTGCCCGGAGTG-3′; Htr6 up-R, SEQ ID NO: 1246 5′-CAGGGGACAGACATCAGTGAG-3′;

UV-Crosslink RIP

UV-crosslink IP was performed using existing methods, except that transcripts in the RNA-protein complexes were not trimmed by RNAse treatment prior to RNA isolation in order to preserve full-length RNA for RT-PCR. Mouse ES cells were UV-irradiated at 254 nm, 400 mJ/cm² (using a Stratagene STRATALINKER), cell nuclei were lysed in RSB-TRITON buffer (10 mM Tris-HCl, 100 mM NaCl, 2.5 mM MgCl₂, 35 μg/mL digitonin, 0.5% triton X-100) with disruptive sonication. Nuclear lysates were pre-cleared with salmon sperm DNA/protein agarose beads for 1 hr at 4° C. and incubated with antibodies overnight. RNA/antibody complexes were then precipitated with Protein A DYNABEADS (Invitrogen), washed first in a low-stringency buffer (1×PBS [150 mM NaCl], 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40), then washed twice in a high-stringency, high-salt buffer (5×PBS [750 mM NaCl], 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40), and treated with proteinase K. RNA was extracted using TRIZOL (Invitrogen) and RT-qPCR was performed as described above.

Expression and Purification of Human PRC2 Components

For expression of human PRC2 subunits, N-terminal flagged-tagged EZH2 and SUZ12 in pFastBac1 were expressed in Sf9 cells. For expression of the whole PRC2 complex, flag-tagged EZH2 was coexpressed with untagged SUZ12, EED, and RBAP48. Extracts were made by four freeze-thaw cycles in BC300 buffer (20 mM HEPES pH 7.9, 300 mM KCl, 0.2 mM EDTA, 10% glycerol, 1 mM DTT, 0.2 mM PMSF, and complete protease inhibitors (Roche)) and bound to M2 beads for 4 h and washed with BC2000 before eluting in BC300 with 0.4 mg/ml flag peptide. EZH2 and PRC2 were adjusted to 100 mM KCl and loaded onto a HiTrap Heparin FF 1 ml column and eluted with a 100-1000 mM KCl gradient. Peak fractions were concentrated using Amicon ultra 10 kDa MWCO concentrators

(Millipore) and loaded onto a Superose 6 column equilibrated with BC300. Peak fractions were collected and concentrated. For SUZ12, the flag elution was concentrated and loaded onto a Superdex 200 column equilibrated with BC300.

Electrophoretic Mobility Shifting Assays (EMSA)

For RNA-EMSA, a 30 nt Hes-1 probe (˜270 bp downstream of TSS in an antisense direction) was used for gel shifts. RNA probes were radiolabeled with [γ-33p]ATP using T4 polynucleotide kinase (Ambion). Purified PRC2 proteins (1 μg) were incubated with labeled probe for 1 hr at 4 C. RNA-protein complexes were separated on a 4% non-denaturing polyacrylamide gel in 0.5×TBE at 250 V at 4° C. for 1 h. Gels were dried and exposed to Kodak BioMax film.

RNA Pulldown Assays

T7 promoter sequence was incorporated into forward primers for PCR products of RepA, Xist exon 1, and truncated Gtl2. Full-length Gtl2 was cloned into pYX-ASC and XistE1 into pEF1/V5/HisB (Invitrogen). Specific primer sequences were:

RepA-F: SEQ ID NO: 1247 TAATACGACTCACTATAGGGAGAcccatcggggccacggatacctgtgtg tcc; RepA-R: SEQ ID NO: 1248 taataggtgaggtttcaatgatttacatcg; Truncated-Gtl2-F: SEQ ID NO: 1249 TAATACGACTCACTATAGGGAGATTCTGAGACACTGACCATGTGCCCAGT GCACC; Truncated-Gtl2-R: SEQ ID NO: 1250 CGTCGTGGGTGGAGTCCTCGCGCTGGGCTTCC; Xist E1-F: SEQ ID NO: 1251 atgctctgtgtcctctatcaga; Xist E1-R: SEQ ID NO: 1252 gaagtcagtatggagggggt;

RNAs were then transcribed using the Mega Script T7 (Ambion), purified using Trizol, and slow-cooled to facilitate secondary structure formation. For pulldown assays, 3 μg of Flag-PRC2 or Flag-GFP and 5 pmol of RNA supplemented with 20U RNAsin were incubated for 30 min on ice. 10 μl of flag beads were added and incubated on a rotating wheel at 4° C. for 1 hr. Beads were washed 3 times with 200 μl buffer containing 150 mM KCl, 25 mM Tris pH 7.4, 5 mM EDTA, 0.5 mM DTT, 0.5% NP40 and 1 mM PMSF. RNA-protein complexes were eluted from flag beads by addition of 35 μl of 0.2M-glycine pH2.5. Eluates were neutralized by addition of 1/10^(th) volume of 1M Tris pH 8.0 and analyzed by gel electrophoresis.

Knockdown Analysis and qRT-PCR

shRNA oligos were cloned into MISSION pLKO.1-puro (Sigma-Aldrich) vector and transfected into wild-type mouse ES cells by Lipofectamine 2000 (Invitrogen). After 10 days of puromycin selection, cells were collected and qRT-PCR was performed to confirm RNA knockdown. The corresponding scrambled sequence (MISSION Non-target shRNA) was used as a control (Scr). The shRNA oligos for Gtl2: (Top strand) 5′-CCG GGC AAG TGA GAG GAC ACA TAG GCT CGA GCC TAT GTG TCC TCT CAC TTG CTT TTT G-3′; SEQ ID NO: 1253 (Bottom strand) 5′-AAT TCA AAA AGC AAG TGA GAG GAC ACA TAG GCT CGA GCC TAT GTG TCC TCT CAC TTG C-3′; SEQ ID NO: 1254. qPCR primers for Gtl2 and Gtl2-as RNAs are as described above. Primers for Dlk1 RNAs: (Forward) 5′-ACG GGA AAT TCT GCG AAA TA-3′; SEQ ID NO: 1255 (Reverse) 5′-CTT TCC AGA GAA CCC AGG TG-3′; SEQ ID NO: 1256. Another Gtl2 shRNA was purchased from Open Biosystems (V2MM_(—)97929). Ezh2 levels after knockdown with this shRNA were tested by qPCR. After testing multiple clones, we concluded that Gtl2 could be knocked down in early passage clones (50-70%), but knockdown clones were difficult to maintain in culture long-term.

DNA ChIP and Real-Time PCR

ChIP was performed as described (Zhao et al., 2008). 5 μl of α-Ezh2 antibodies (Active Motif 39103), normal rabbit IgG (Upstate 12-370), and α-H3K27me3 (Upstate) were used per IP. Real-time PCR for ChIP DNA was performed at the Gtl2-proximal DMR with prGtl2F/prGtl2R, at the Gtl2-distal DMR with DMR-F/DMR-R, at the Dlk1 promoter with prDlk1F/prDlk1R, and at the Gapdh promoter with prGAPDH-F/prGAPDH-R. Primer sequences are as follows:

proximal-DMR SEQ ID NO: 1257 5′-CATTACCACAGGGACCCCATTTT; proximal-DMR SEQ ID NO: 1258 5′-GATACGGGGAATTTGGCATTGTT; prDlk1F SEQ ID NO: 1259 5′-CTGTCTGCATTTGACGGTGAAC; prDlk1R SEQ ID NO: 1260 5′-CTCCTCTCGCAGGTACCACAGT; distal-DMR-F SEQ ID NO: 1261 5′-GCCGTAAAGATGACCACA; distal-DMR-R SEQ ID NO: 1262 5′-GGAGAAACCCCTAAGCTGTA; prGAPDH-F SEQ ID NO: 1263 5′-AGCATCCCTAGACCCGTACAGT; prGAPDH-R SEQ ID NO: 1264 5′-GGGTTCCTATAAATACGGACTGC; prActin-F SEQ ID NO: 1265 5′-GCA GGC CTA GTA ACC GAG ACA; prActin-R SEQ ID NO: 1266 5′-AGT TTT GGC GAT GGG TGC T;

The following materials and methods were used in Examples 6-10 set forth below.

LNA Nucleofection—2×10⁶ SV40T transformed MEFs were resuspended in 100 μl of Mef nucleofector solution (Lonza). Cy3-labeled LNA molecules were added to a final concentration of 2 μM. The cells were transfected using the T-20 program. 2 ml of culture medium was added to the cells and 100 μl of this suspension was plated on one gelatinized 10 well slide per timepoint. LNA sequences were designed using Exiqon software (available at exiqon.com). Modified LNA bases were strategically introduced to maximize target affinity (Tm) while minimizing self-hybridization score. The LNA molecule sequences (from 5′ to 3′) were as follows:

LNA-Scr, GTGTAACACGTCTATACGCCCA; SEQ ID NO: 1267 LNA-C1, CACTGCATTTTAGCA; SEQ ID NO: 1268 LNA-C2, AAGTCAGTATGGAG; SEQ ID NO: 1269 LNA-B, AGGGGCTGGGGCTGG; SEQ ID NO: 1270 LNA-E, ATAGACACACAAAGCA; SEQ ID NO: 1271 LNA-F, AAAGCCCGCCAA; SEQ ID NO: 1272 LNA-4978, GCTAAATGCACACAGGG; SEQ ID NO: 1273 LNA-5205, CAGTGCAGAGGTTTTT; SEQ ID NO: 1274 LNA-726, TGCAATAACTCACAAAACCA; SEQ ID NO: 1275 LNA-3′, ACCCACCCATCCACCCACCC; SEQ ID NO: 1276

Real Time PCR —

Total RNA was extracted after nucleofection using Trizol (Invitrogen). Reverse transcriptase reaction was performed using the Superscript II kit and real time PCR performed on cDNA samples using icycler SYBR green chemistry (Biorad).

ChIP—

Cells were fixed at various time points after nucleofection in 1% formaldehyde solution. Fixation was stopped by addition of glycine to 0.125M and ChIP was performed as described earlier (28) and quantitated by qPCR.

Antibodies—

The antibodies for various epitopes were purchased as follows: H3K27me3, Active Motif 39535. Ezh2, Active Motif 39639 and BD Pharmingen 612666. For Immunostaining, H3K27me3 antibodies were used at 1:100 dilution and Ezh2 antibodies (BD Pharmingen) at 1:500. Alexa-Fluor secondary antibodies were from Invitrogen. For Western blots, Ezh2 antibodies (BD Pharmingen) were used at 1:2000 dilution. Actin antibody (Sigma A2066) was used at 1:5000 dilution.

DNA FISH, RNA FISH, and Immunostaining—

Cells were grown on gelatinized glass slides or cytospun. RNA FISH, DNA FISH, serial RNA-DNA FISH, immunostaining, and immunoFISH were performed based on existing methods. Xist RNA FISH was performed using nick-translated pSx9-3 probe or an Xist riboprobe cocktail. pSx9-3 was used as probe for Xist DNA FISH. For metaphase spreads, colchicine was added to cells for 1 hr. Cells were trypsinized and resuspended in 3 ml of 0.056M KCl for 30 minutes at room temperature, centrifuged and resuspended in methanol:acetic acid (3:1) fixative. After several changes of fixative, cells were dropped on a chilled slide and processed for RNA or DNA FISH.

Example 1 Capturing the PRC2 Transcriptome by RIP-seq

A method of capturing a genome-wide pool of RNA bound to PRC2 was developed by combining two existing methods native RIP and RNA-seq (this method is referred to herein as “RIP-seq”). Nuclear RNAs immunoprecipitated by α-Ezh2 antibodies were isolated from mouse ES cells and an Ezh2−/− control, cDNAs created using strand-specific adaptors, and those from 200-1,200 nt were purified and subjected to Illumina sequencing.

In pilot experiments, we performed RIP on 10⁷ ES cells and included several control RIPs to assess the specificity of α-Ezh2 pulldowns. In the wildtype pulldown and its technical and biological replicates, α-Ezh2 antibodies precipitated 70-170 ng of RNA from 107 ES cells and yielded a cDNA smear of >200 nt. Treatment with RNAses eliminated products in this size range and −RT samples yielded no products, suggesting that the immunoprecipitated material was indeed RNA. There was ˜10-fold less RNA in the Ezh2−/− pulldown (˜14 ng) and when wildtype cells were immunoprecipitated by IgG (˜24 ng). A 500-fold enrichment over a mock RIP control (no cells) was also observed. In the >200 nt size range, control RIPs (null cells, IgG pulldowns, mock) were even further depleted of RNA, as these samples were dominated by adaptor and primer dimers. Adaptor/primer dimers, rRNA, mitochondrial RNA, reads with <18 nt or indeterminate nucleotides, and homopolymer runs in excess of 15 bases were computationally filtered out. From an equivalent number of cells, control RIPs were significantly depleted of reads. In wildtype libraries, 231,880-1.2 million reads remained after filtering. By contrast, only 4,888 to 73,691 reads remained in controls. The overwhelming majority of transcripts in the controls were of spurious nature (adaptor/primer dimers, homopolymers, etc.). Therefore, wildtype RIPs exhibited substantial RNA enrichment and greater degrees of RNA complexity in comparison to control RIPs.

Approximately half of all reads in the wildtype libraries was represented three times or more. Even after removing duplicates to avoid potential PCR artifacts, the wildtype library contained 301,427 distinct reads (technical and biological replicates with 98,704 and 87,128, respectively), whereas control samples yielded only 1,050 (IgG) and 17,424 (null). The wildtype libraries were highly similar among each other, with correlation coefficients (CC) of 0.71-0.90, as compared to 0.27-0.01 when compared against Ezh2−/− and IgG controls, respectively. Reads mapping to repetitive elements of >10 copies/genome accounted for <20% of total wildtype reads, with simple repeats being most common and accounting for 85.714%, whereas LINEs, SINEs, and LTRs were relatively under-represented. Because reads with <10 alignments have greatest representation, we hereafter focus analysis on these reads (a cutoff of <10 retains genes with low-copy genomic duplications).

Genome distributions were examined by plotting distinct reads as a function of chromosome position. Alignments showed that PRC2-associated RNAs occurred on every chromosome in the wildtype libraries. Alignments for IgG and Ezh2−/− controls demonstrated few and sporadic reads. Therefore, our RIP-seq produced a specific and reproducible profile for the PRC2 transcriptome. A large number of wildtype reads hits the X-chromosome, and a zoom of the X-inactivation center showed that our positive controls—Tsix, RepA, and Xist RNAs—were each represented dozens of times. The high sensitivity of RIP-seq detection was suggested by representation of RepA and Xist, which are in aggregate expressed at <10 copies/ES cell. On the other hand, no hits occurred within other noncoding RNAs of the X-inactivation center. Thus, the RIP-seq technique was both sensitive and specific.

Example 2 The PRC2 Transcriptome

To obtain saturating coverage, sequencing was scaled up and 31.9 million reads were obtained for the original wildtype sample and 36.4 million for its biological replicate. After removing duplicates and filtering 1,030,708 and 852,635 distinct reads of alignment ≦10 remained for each library, respectively. These reads were then combined with pilot wildtype reads for subsequent analyses (henceforth, WT library) and all analyses were performed using the Ezh2−/− library as control.

A strategy was designed based on the relative representation in the WT versus null libraries, reasoning that bona fide positives should be enriched in the WT. Genic representations were calculated using “reads per kilobase per million reads” (RPKM) as a means of normalizing for gene length and depth of sequencing, and then all 39,003 transcripts in the UCSC joined transcriptome were mapped to a scatterplot by their WT RPKM (x-axis) and their null RPKM (y-axis) values. Transcripts with zero or near-zero representation in both libraries accounted for the vast majority of datapoints [blue cloud at (0,0)]. Transcripts with nonzero x-values and a zero y-value indicated a population represented only in WT pulldowns. To determine an appropriate enrichment threshold, we performed an in silico subtraction. WT/null RPKM ratios were examined for the same calibrators. Xist/RepA scored 4.18/0, implying hundreds to thousands of representations in the WT library but none in the null. Tsix scored 10.35/3.27, Bsn pasr 0.95/0, and Kcnq1ot1 1.17/0. The negative controls scored low ratios, with Pax3-pasr at 0.11/0.26, Hey1-pasr 0.28/0, Hotair 0.25/0, Insl6 0.27/3.09, and Ccdc8 0.22/5.04. On this basis, a 3:1 enrichment ratio for RPKM(WT)/RPKM(null) and a minimum RPKM of 0.4 were called.

Transcript identification for the “PRC2 transcriptome” was based on the fact that there are ˜10-times more RNAs pulled down by EZH2 antibodies in the wildtype cell line than in the Ezh2-null line, indicating that the wildtype library is highly enriched for PRC2-associated transcripts and that no further in silico subtraction is necessary. Using this criterion, the size of the expanded PRC2 transcriptome is estimated at −57K RNAs.

Example 3 Identification of PRC2-Binding Peaks (PRC2-Associated Regions) from Appendix I

In some or any embodiments, the region of an RNA to which a protein binding partner (e.g., PRC2) binds is one of the exemplary locations on a target lncRNA to which a single stranded oligonucleotide is designed to hybridize. For example, these regions can be identified by reviewing the data in Appendix I and identifying regions that are enriched in the dataset; these regions are likely to include PRC2-binding sequences.

The sequence reads in Appendix I come directly off the Illumina GA-II genome analyzer and are in an orientation that is the reverse complement of the PRC2-binding transcript. Appendix I is a filtered subset of all of the reads after bioinformatic filtering removed adaptor/primer dimers, mitochondrial RNA, rRNA, homopolymers, reads with indeterminate nucleotides, and truncated reads (<15nt). They are likely to represent regions best protected from endogenous nucleases during RIP and subsequent RNA purification steps described in Example 1 above (a RIP-seq method) and thus represent candidate regions of RNA that bind to PRC2 or associated proteins or complexes. From Appendix I, reads were extracted corresponding to transcripts that are enriched 3:1 in WT vs. null [RPKM(WT)/RPKM(null)≧3.0] and with a minimal RPKM value of 0.4. Regions of the PRC2-binding transcripts with an uninterrupted pile-up of reads (peaks) were identified and considered candidate PRC2 contact regions within the RNA.

The sequence reads in Appendix I were used to generate sequence coverage on the reference genome using the Broad Institute's Arachne aligner, ShortQueryLookup, which is based on making a k-mer (K=12) dictionary of the reference genome and performing a local Smith-Waterman alignment on a read's candidate locations based on matching k-mer locations in the genome. The aligner does multiple placements. The best alignment is allowed to have at most one error and alignments that differ from the best alignment's number of errors by one are also accepted. The coverage is normalized by dividing by the number of places the read aligns (e.g. if a reads aligns to four places, 0.25 is added to each of the bases in the four places).

To obtain the target Peaks, the following methodology was used. A base-level mouse (mm9) coverage file of regions where the wild-type coverage of the transcriptome is enriched at least three-fold over the coverage of the Ezh2−/− transcriptome and has a minimum RPKM coverage of at least 0.4 serves as the starting point. The coverage is strand-specific. Next, in non-overlapping consecutive windows of 100 bps in length, peak values and their locations are determined. Peak positions are then corrected for those peaks that are on the edge of a window that are determined to be on a side of a larger peak. Those peaks are moved to the top of the larger peak. Duplicate peak locations are then removed. Peaks positions that are on a plateau are moved to the center of the plateau. The coverage is then smoothed using a Gaussian kernel, (1/sqrt(2*sigma*pi))*exp(−t̂2/(2*sigma)), where sigma=5.0. Peak widths are then determined by locating the nearest position to the peak such that the smoothed coverage is less than or equal to one-third the maximum coverage. Adjacent peaks that overlap each other are resolved by placing a boundary between them at the midpoint between the peaks. Peaks are then output into a table with the position, width, the maximum amplitude, and the sum of unsmoothed coverage underneath the width of the peak. The corresponding nucleotide sequences of the mouse Peaks in mm9 (converted to RNA by replacing T with U) appear in sequences B47,408 to B616,428 [mouse Peaks]. Mouse-to-human LiftOver of the mouse chromosome coordinates and strand of these mouse Peaks was performed in the UCSC genome browser as described herein, to generate orthologous human chromosome coordinates. This process and LiftOver chains is known in the art. When the mouse coordinates (mm9) of each mouse Peak were converted to the corresponding human (hg19) coordinates, mapping percentages of 50, 65, 75, and 95 yielded essentially identical location and length results whenever a match occurred. Consequently, the 50% mapping parameter was used.

Each corresponding human Peak RNA sequence (i.e., the nucleotide sequence of the human chromosomal coordinates and strand, converted to RNA by replacing T with U) appear in sequences B652,256 to B916,209 [human Peaks]. Table 1 displays the mouse sequences and the corresponding human sequences. These human Peaks and the human PRC2 transcriptome (i.e. human sequences of PRC2-binding transcripts) were intersected with known genes from the NCBI database to identify genes targeted by the PRC2-binding RNA (i.e. an intersecting or nearby gene).

Table 2 of International Patent Application Publication WO/2012/087983 shows the annotation of the mouse and human Peaks with the names of genes that were near or intersected with each Peak. The unique NCBI gene ID associated with the human gene (listed first) or mouse gene (listed second) appears in parentheses adjacent to the gene name. The degree of overlap between the Peak coordinates and the gene coordinates appears in square brackets. A positive number indicates the number of overlapping nucleotides between the two, and a negative number represents the size of the gap between the two (i.e. the number of nucleotides of distance between the two). For Peaks, an “F” within the square brackets indicates that the Peak coordinates fully overlap the gene coordinates. For transcripts, an “F” within the square brackets indicates that the transcript coordinates fully overlap the gene coordinates, or vice versa. The RNA transcript or Peak is “antisense” to the reference genes in the “Opposite Strand” column, while the RNA transcript or Peak is in the same “sense” orientation as the reference gene in the “Same Strand” column.

Bioinformatic analysis indicates that the average Peak is about 40-60 bases, which is an excellent size for initial design of single stranded oligonucleotides. Each of these Peaks is fully represented by the reverse-complement reads in Appendix I since it corresponds to a segment of overlapping reverse-complement reads from Appendix I. The Peaks can be found anywhere within the coding gene, and in either sense or antisense orientations. Peaks can also be found in the promoter/5′UTR regions, introns, internal exons, and 3′UTR and beyond. The analysis strongly suggests that the PRC2-interacting transcripts are not the protein-coding mRNA, but a distinct transcript or transcripts that overlap with the mRNA sequence. Many are novel RNAs not previously described.

Methods disclosed herein can be used to design a single stranded oligonucleotide that binds to target locations or segments with sufficient specificity, or are sufficiently complementary to the target RNA to give the desired effect. In some embodiments, the methods include using bioinformatics methods known in the art to identify regions of secondary structure, e.g., one, two, or more stem-loop structures, or pseudoknots, and selecting those regions to target with a single stranded oligonucleotide.

Additional target segments 5-500 nucleotides in length, or about 5 to about 100 nucleotides in length, or about 2 kb in length, comprising a stretch of at least five (5) consecutive nucleotides within the Peak, or immediately adjacent thereto, are considered to be suitable for targeting as well.

For each of the human Peaks that did not match a longer human transcript sequence, a longer 2 kb fragment of surrounding human chromosomal sequence was identified, and appears in sequences B916,626-B934,761 [larger region surrounding human Peaks].

Example 4 Evidence Supporting Direct Binding of RNA to PRC2 in or Around the Peak Regions

Experiments were carried out to test the idea that RNA identified using the criteria in Example 2 directly bind PRC2. In vitro biochemical analyses were performed using purified recombinant human PRC2 subunits, EED, EZH2, SUZ12, and RBAP48. The newly identified antisense RNA for Hes1 (a transcription factor in the Notch signaling pathway contains a double stem-loop structure, a motif also found in RepA. In an RNA electrophoretic mobility shift assay (EMSA), both the 28-nt RepA and 30-nt Hes1-as probes were shifted by PRC2, whereas RNAs derived from other regions of Xist (DsI, DsII) were not. Mutating the stem-loop structures reduced PRC2 binding. To determine which subunit of PRC2 binds Hes1-as, we performed EMSA using specific subunits. EZH2 strongly shifted wildtype but not mutated Hes1-as RNA, whereas neither SUZ12 nor EED shifted Hes1-as. The RNA-protein shift was always more discrete when whole PRC2 was used, suggesting that other subunits stabilize the interaction.

These results show that Hes1-as RNA directly and specifically interacts with PRC2 and Ezh2 is the RNA-binding subunit. Further evidence comes from the observation that the two of the greatest peaks within the Xist/Tsix locus localize to the Repeat A region, the 28-nt repeated motif known to directly interact with EZH2 on both the forward and reverse strands. RNA fragments derived from “Peaks” showed robust shifts with PRC2, whereas those mapping outside the “Peaks” shifted poorly. We therefore believe that many, if not all, of the identified “Peaks” of Table 2 of International Patent Application Publication WO/2012/087983 represent bona fide PRC2-interacting domains of the RNA. These results show that the Peaks, and likely adjacent regions, directly and specifically interact with PRC2 complex.

Example 5 In Vitro Effect of Single Stranded Oligonucleotides on Upregulation of mRNA Expression

A. ApoE

Single stranded oligonucleotides were designed to target lncRNA in order to upregulate ApoE. The oligonucleotides were less than 16 bases in length and comprised unmodified DNA and multiple locked nucleic acid modified bases, all linked by phosphorothioate bonds. Transfection and data analysis were carried out briefly as follows.

RNA was harvested from the Hep 3B cells using Promega SV 96 Total RNA Isolation system omitting the DNAse step. In separate pilot experiments, 50 ng of RNA was determined to be sufficient template for the reverse transcriptase reaction. RNA harvested from the Hep3B cells was normalized so that 50 ng of RNA was input to each reverse transcription reaction. For the few samples that were too dilute to reach this limit, the maximum input volume was added. Quantitative PCR evaluation was then completed.

A baseline level of ApoE mRNA expression was determined through quantitative PCR as outlined above. Baseline levels were also determined for mRNA of various housekeeping genes which are constitutively expressed. A “control” housekeeping gene with approximately the same level of baseline expression as ApoE mRNA was chosen for comparison purposes to ApoE.

Hep3B cells were seeded into each well of 24-well plates at a density of 25,000 cells per 500 uL and transfections were performed with Lipofectamine and the single stranded oligonucleotides. Control wells contained Lipofectamine alone. At 48 hours post-transfection, approximately 200 uL of cell culture supernatants were stored at −80 C for ELISA. At 48 hours post-transfection, RNA was harvested from the Hep 3B cells and quantitative PCR was carried out as outlined above. The percent induction of ApoE mRNA expression by each single stranded oligonucleotide was determined by normalizing mRNA levels in the presence of the single stranded oligonucleotide to the mRNA levels in the presence of control (Lipofectamine alone). This was compared side-by-side with the increase in mRNA expression of the “control” housekeeping gene.

A total of 26 oligonucleotides tested were complementary to PRC2-binding RNA sequences identified according to Example 2 above. Of these 26 oligonucleotides, 7 upregulated apoE expression in human Hep3B cells, as indicated by increased ApoE mRNA levels relative to the “control” housekeeping gene.

The above procedure was repeated using human renal proximal tubule epithelial cells (RPTEC). Of the 26 oligonucleotides complementary to PRC2-binding RNA sequences identified according to Example 2 above, 5 increased ApoE mRNA levels in renal cells, relative to the “control” housekeeping gene. Levels increased by about 1.5 to about 5-fold over baseline expression.

In addition, of 11 oligonucleotides that are complementary to Peaks associated with apoE identified according to Example 3 above, 3 upregulated apoE expression.

Single stranded oligonucleotides as short as 8 nucleobases in length were demonstrated to upregulate gene expression.

B. Nkx2-1

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA in order to upregulate Nkx2-1. A total of 13 oligonucleotides tested were complementary to a PRC2-binding RNA sequence identified according to Example 2 above. Of these 13 oligonucleotides, 3 upregulated Nkx2-1 expression as indicated by increased Nkx2-1 mRNA expression relative to baseline, although no “control” housekeeping gene could be matched with Nkx2-1 due to low levels of intrinsic expression. In addition, of 9 oligonucleotides that are complementary to Peaks associated with Nkx2-1 identified according to Example 3 above, 3 upregulated Nkx-21 expression.

C. Brca1

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA in order to upregulate Brca1. A total of 30 oligonucleotides tested were complementary to two PRC2-binding RNA sequences identified according to Example 2 above. Of these 30 oligonucleotides, 5 oligonucleotides upregulated Brca1 expression. Of these 30 oligonucleotides, 13 oligonucleotides were also complementary to Peaks associated with Brca1 identified according to Example 3 above. Of these 13 oligonucleotides complementary to Peaks, 2 oligonucleotides upregulated Brca1 expression. Levels increased by about 2 to about 3 fold over baseline expression.

D. Smad7

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA as set forth in the sequence listing in order to upregulate Smad7, with the following exception: the kidney cell line RPTEC was used instead of HepB3. A total of 28 oligonucleotides tested were complementary to sequence B18602. Of these 28 oligonucleotides, 4 upregulated Smad7 expression. In addition, of 28 oligonucleotides that are complementary to Peaks in Table 2 of International Patent Application Publication WO/2012/087983 associated with Smad7, 4 upregulated Smad7 expression.

E. SirT6

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA in order to upregulate SirT6. A total of 25 oligonucleotides tested were complementary to a PRC2-binding RNA sequence identified according to Example 2 above. Of these 25 oligonucleotides, 3 upregulated SirT6 expression. A total of 2 oligonucleotides tested were complementary to another PRC2-binding RNA sequence identified according to Example 2 above. Of these 2 oligonucleotides, 1 upregulated SirT6 expression. A total of 2 oligonucleotides tested were complementary to another PRC2-binding RNA sequence identified according to Example 2 above. Of these 2 oligonucleotides, neither upregulated SirT6 expression. Levels increased by 2 to 6 fold over baseline expression. In addition, of 6 oligonucleotides that are complementary to Peaks associated with SirT6 identified according to Example 3 above, 1 upregulated SirT6 expression.

F. SerpinF1

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA in order to upregulate SerpinF1. A total of 38 oligonucleotides tested were complementary to two PRC2-binding RNA sequences identified according to Example 2 above. Of these 38 oligonucleotides, 3 upregulated SerpinF1 expression. Levels increased by 1.2 to 2 fold over baseline expression. In addition, of 32 oligonucleotides that are complementary to Peaks associated with SerpinF1 identified according to Example 3 above, 3 upregulated SerpinF1 expression.

G. KLF1

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA as set forth in Table 2 of International Patent Application Publication WO/2012/087983 in order to upregulate KLF1. A total of 30 oligonucleotides tested were complementary to sequences B15688 and B15689 in Table 2 of International Patent Application Publication WO/2012/087983. Of these 30 oligonucleotides, 15 upregulated KLF1 expression in human Hep3B cells, as indicated by increased KLF1 mRNA levels relative to the “control” housekeeping gene. In addition, of 2 oligonucleotides that are complementary to Peaks in Table 2 of International Patent Application Publication WO/2012/087983 associated with KLF1, 1 upregulated KLF1 expression. Levels increased by 2 to 50 fold over baseline expression.

H. Rps19

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA as set forth in Table 2 of International Patent Application Publication WO/2012/087983 in order to upregulate rps19. A total of 30 oligonucleotides tested were complementary to sequences B630259 and B630260. Of these 30 oligonucleotides, 7 upregulated rps19 expression as indicated by increased rps19 mRNA expression relative to the “control” housekeeping gene. In addition, of 25 oligonucleotides that are complementary to Peaks in Table 2 of International Patent Application Publication WO/2012/087983 associated with rps19, 7 upregulated Rps19 expression. Levels increased by 1.2 to 1.6 fold over baseline expression.

I. PTEN

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA as set forth in Table 2 of International Patent Application Publication WO/2012/087983 in order to upregulate PTEN. A total of 40 oligonucleotides tested were complementary to sequences B650,560 and B650,559 in Table 2 of International Patent Application Publication WO/2012/087983. Of these 40 oligonucleotides, 18 oligonucleotides upregulated PTEN expression. Of these 40 oligonucleotides, 31 were also complementary to Peaks in Table 2 of International Patent Application Publication WO/2012/087983 associated with PTEN. Of these 31 oligonucleotides complementary to Peaks, 11 oligonucleotides upregulated PTEN expression. Levels increased by about 1.5 to about 5 fold over baseline expression.

J. EPO

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA as set forth in Table 2 of International Patent Application Publication WO/2012/087983 in order 111 to upregulate erythropoietin (EPO). A total of 13 tested oligonucleotides were complementary to sequences B932,189 or B932,190. Of these 13 oligonucleotides, 5 upregulated EPO expression. In addition, of 2 oligonucleotides that are complementary to Peaks in Table 2 of International Patent Application Publication WO/2012/087983 associated with EPO, 1 upregulated EPO expression. Levels increased by 4 fold over baseline expression.

An ELISA assay using a commercially available kit [DEP00, RnD Systems] was used according to the manufacturer's instructions to determine secreted protein present in cellular supernatant. Fold induction of protein was determined by normalizing protein levels induced by oligonucleotides to the protein levels induced by control (Lipofectamine alone). The data showed that of the 1 oligonucleotides tested that increased EPO mRNA expression, it demonstrated a corresponding EPO protein expression increase. 3 oligonucleotides complementary to sequences B14486 and B14487 (transcripts that overlap the mouse EPO gene) were tested in vivo for ability to upregulate mouse EPO expression.

In addition, two other oligos targeting downstream peak regions were tested as well. Of these, 4 oligonucleotides were complementary to Peak regions in Table 2 of International Patent Application Publication WO/2012/087983 associated with EPO. Male C57B16/J mice [6-8 wks old and 20-25 g] were administered subcutaneously a single injection of oligonucleotide, at a dose of either 10 mg/kg or 25 mg/kg in 100 μl of sterile phosphate buffered saline.

At a time point 48 hours after injection, terminal blood samples were taken via cardiac puncture and assayed for levels of EPO protein using an ELISA assay [MEP00, RnD Systems] according to the manufacturer's instructions. Of the oligos tested that were complementary to sequence B14486 or B14487 or Peaks, one demonstrated a 5-fold induction and another demonstrated a 7-fold induction of EPO protein at a dose of 25 mg/kg. Of these two oligonucleotides that induced EPO protein expression in vivo, one is within 150 bases of (and the other is within 1500 bases of) and both are on the opposite strand as the mouse Peak that is sequence B461812. This mouse Peak corresponds to the human Peak of sequence B845472.

K. BDNF

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA as set forth in Table 2 of International Patent Application Publication WO/2012/087983 in order to upregulate BDNF. A total of 21 oligonucleotides tested were complementary to sequences B620236 and B620237. Of these 21 oligonucleotides, 9 upregulated BDNF expression. A total of 2 oligonucleotides tested were complementary to sequence B130,694. Of these 2 oligonucleotides, 1 upregulated BDNF expression. Levels increased by 1.5 to 6 fold over baseline expression. In addition, of 14 oligonucleotides that are complementary to Peaks in Table 2 of International Patent Application Publication WO/2012/087983 associated with BDNF, 6 upregulated BDNF expression. Levels increased by 2 to 7 fold over baseline expression.

L. Granulin

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA as set forth in Table 2 of International Patent Application Publication WO/2012/087983 in order to upregulate Granulin. A total of 30 oligonucleotides tested were complementary to sequence B640164 and B192311. Of these 30 oligonucleotides, 6 upregulated Granulin expression as indicated by increased Granulin mRNA expression relative to the “control” housekeeping gene. In addition, of 22 oligonucleotides that are complementary to Peaks in Table 2 of International Patent Application Publication WO/2012/087983 associated with Granulin, 4 upregulated Granulin expression. Levels increased by 1.5 to 2 fold over baseline expression.

M. KLF4

A total of 30 oligonucleotides tested were complementary to sequence B624099. Of these 30 oligonucleotides, 13 upregulated KLF1 expression in human Hep3B cells, as indicated by increased KLF4 mRNA levels relative to the “control” housekeeping gene. In addition, of 20 oligonucleotides that are complementary to Peaks in Table 2 of International Patent Application Publication WO/2012/087983 associated with KLF4, 10 upregulated KLF4 expression. Levels increased by 2 to 15 fold over baseline expression.

N. Fvii (Factor VII)

The experiments as described in Example 5A above were repeated for single stranded oligonucleotides designed to target lncRNA as set forth in Table 2 of International Patent Application Publication WO/2012/087983 in order to upregulate Fvii. The oligonucleotides designed to target Fvii were about 20 bases in length and comprised modified DNA with a 2′-0-Me with full phosphorothioate linkage backbone. A total of 25 oligonucleotides tested were complementary to sequences B632564 and B632565 in Table 2 of International Patent Application Publication WO/2012/087983. Of these 25 oligonucleotides, 12 upregulated Fvii expression. Levels increased by 2- to 25 fold over baseline expression. In addition, of 25 oligonucleotides that are complementary to Peaks in Table 2 of International Patent Application Publication WO/2012/087983 associated with Fvii, 12 upregulated Fvii expression.

Example 6 LNA Molecules Targeting Xist Repeat C Rapidly Displace Xist RNA from Xi

Repeat C was aligned using Geneious (Geneious v5.1, Available on the internet at geneious.com) and LNA molecules complementary to two regions with a high degree of inter-repeat conservation were synthesized. The first LNA molecule showed conservation in all 14 repeats (LNA-C1) and the second in 13 of 14 (LNA-C2). LNA molecules were nucleofected separately into transformed mouse embryonic fibroblasts (MEFs), and the cells were adhered onto slides and fixed in situ at various timepoints between 0 minutes (immediately after nucleofection) and 8 hours post-nucleofection. To examine effects on Xist RNA, RNA fluorescence in situ hybridization (FISH) was performed using Xist-specific probes. (MEF cells are tetraploid due to transformation; each tetraploid cell has two Xa and two Xi). In controls transfected with scrambled LNA molecules (LNA-Scr), robust Xist clouds were seen in 80-90% of cells at all timepoints. Intriguingly, introduction of either LNA-C1 or -C2 resulted in immediate loss of Xist RNA from Xi. Even at t=0 (cells fixed immediately, within seconds to minutes, after LNA introduction), ˜10% of nuclei displayed a loosening of the Xist RNA clusters, with the clusters appearing faint and diffuse. The percentage of nuclei with full Xist clouds continued to drop during the first hour and reached a minimum at t=60 minutes (21%, n=190). These findings indicate that LNA molecules disrupted Xist binding to chromatin as soon as they were introduced. However, the loss of Xist from Xi was transient, as pinpoints of Xist RNA typical of nascent transcripts seen in undifferentiated embryonic stem (ES) cells, became visible at t=3 hr. Full recovery of Xist clouds was not seen until 8-24 hr post-nucleofection (81% at 8 hr, n=117).

The next experiment addressed whether LNA molecules had similar effects in mouse ES cells an established ex vivo model which recapitulates XCI as the cells differentiate in culture. In the undifferentiated state, wildtype female ES cells express low levels of Xist RNA, visible as pinpoint signals by RNA FISH. By day 6 of differentiation, ˜40% of cells would normally have upregulated Xist RNA. When ES cells were nucleofected with LNA-C1 on day 6, Xist displacement occurred rapidly, reaching a maximum at 1 hr and recovering by 8 hr. Thus, LNA molecules were effective in ES cells as well as in somatic cells. These results contrasted sharply with those obtained from MEFs nucleofected with siRNAs or shRNAs toward the same region of Xist. Neither siRNAs nor shRNAs led to loss of Xist at the 1, 3 or 24 hour timepoints, and partial decreases in Xist clouds occurred only at 48 hours (83%, n=84 at 1 hr; 80%, n=106 at 24 hr). Thus, LNA molecules can be used efficiently to target long nuclear ncRNAs such as Xist with extremely rapid kinetics, much more rapid than the action of siRNAs or shRNAs, in multiple cell types.

To test the specificity of the LNA molecules, human 293 cells were nucleofected with the Repeat C LNA molecules. Sequence comparison between the mouse and human Xist/XIST revealed that the region targeted by LNA-C1 is conserved in 10 of 15 nt and is conserved in 10 of 14 nt for LNA-C2. Nucleofection of scrambled LNA molecules followed by XIST RNA FISH in human cells showed two normal XIST clouds in nearly all cells (92%, n=108). Similarly, nucleofection with either LNA-C1 or LNAC-2 did not change the XIST clouds (LNA-C1, 89%, n=126; LNA-C2, 85%, n=139). Thus, mouse Repeat C LNA molecules do not affect human XIST localization, suggesting that they function in a species-specific manner. To determine whether human Repeat C could displace human XIST, we nucleofected LNA molecules complementary to the human Repeat C into 293 cells, but observed no loss of XIST clouds (91%, n=103 at 1 hr; 87%, n=95 at 3 hr and 92%, n=85 at 8 hr). This finding indicated that, although Repeat C may play a role in humans, additional human elements function in RNA localization. Whereas mouse Repeat C occurs 14 times, the human repeat is present only once.

Example 7 Xist RNA is Displaced without Transcript Destabilization

Several mechanisms could explain the disappearance of Xist. LNA molecules could anneal to the complementary region and target Xist for degradation. Alternatively, hybridization to LNA molecules could displace Xist RNA from Xi without affecting the transcript stability. To distinguish between these possibilities, Xist levels were quantitated relative to Gadph levels (control) by qRT-PCR at different timepoints. At 1 hr when Xist clouds were no longer visible, Xist levels remained comparable to that seen in the scrambled control. Even at 3 and 8 hr, Xist levels did not change significantly. These results showed that displacement of Xist occurred without complete RNA degradation. Thus, LNA molecules function by blocking Xist interaction with chromatin rather than altering the RNA's stability.

The rapid displacement of Xist and the slow kinetics of recovery provided the opportunity to investigate several unanswered questions regarding Xist's mechanism of localization. To ask whether reappearance of Xist on Xi is due to relocalization of displaced Xist molecules or to coating by newly synthesized RNA, we performed time-course analysis in the presence of actinomycin D (ActD), an inhibitor of RNA polymerase II. Previous studies have shown that the half-life of Xist in the cell is approximately 4-6 hr. It was reasoned that treating cells with ActD for 0-8 hr would prevent new synthesis of Xist RNA during this timeframe and that, therefore, reappearance of Xist clouds would imply relocalization of displaced RNA back onto Xi. LNA molecules were introduced into cells and then the cells were allowed to recover in medium containing ActD. In the scrambled controls, Xist clouds were clearly visible at all time points without ActD. With ActD, Xist clouds were apparent in the 1 and 3 hr timepoints and were lost by 8 hr, consistent with a 4-6 hr half-life. In LNA-C1- or LNA-C2-treated samples allowed to recover without ActD, pinpoints of Xist were visible at 3 hr and Xist clouds were restored by the 8 hr timepoint. However, with ActD, Xist clouds were never restored, neither fully nor partially. Thus, Xist recovery after LNA molecule-mediated displacement from Xi is due to new RNA synthesis and not relocalization of the displaced transcript.

Example 8 Xist RNA Localizes Near the X-Inactivation Center First

Taking further advantage of the rapid displacement and slow recovery, the long-standing question of whether Xist spreads in a piecemeal fashion or localizes simultaneously throughout Xi was asked. One hypothesis is that coating initiates near the Xist locus and proceeds to both ends of the chromosome through booster elements located along the X. Alternatively, coating can occur all at once through multiple X-linked seeding points which would promote local spreading. Xist localization on metaphase chromosomes was analyzed during the 3-8 hr period of recovery. In cells treated with scrambled LNA molecules, all metaphase chromosomes coated with Xist RNA showed a banded pattern similar to the heterogeneous patterns described in earlier works. By contrast, LNA-C1 treated cells gave intermediate patterns. At 1 hr, no metaphase chromosomes showed a coat of Xist RNA (0%, n=41). At 3 hr when Xist RNA could be seen as a pinpoint in interphase cells, the predominant pattern was a combination of a single bright band in the middle of the metaphase chromosome together with a small number of very faint bands elsewhere on the X (52%, n=46). This result suggested that Xist RNA initially bound locally. To determine whether the strong RNA band was localized to the Xist region, Xist RNA FISH was carried out on non-denatured nuclei and followed with denaturation and hybridization to an Xist probe. Indeed, the focal RNA band observed at the 3-hr mark colocalized with the Xist region. At 5 hr, intermediate degrees of coating and intensities could be seen (68%, n=38). At 8 hr, the predominant pattern was the whole-chromosome painting pattern typical of control cells (78%, n=38). In controls, intermediate patterns were not observed at any time. These findings argue that Xist RNA initially binds nearby, but seems to spread to the rest of Xi at the same time, within the temporal and spatial resolution of the FISH technique.

Example 9 Xist RNA Displacement is Accompanied by Loss of PRC2 Localization

The pattern of Polycomb repressive complex 2 (PRC2) binding to Xi has been of considerable interest, as its Ezh2 subunit catalyzes trimethylation of Histone H3 at lysine 27 (H3K27me3). Several studies have shown that PRC2 localizes to Xi in an Xist-dependent manner, as deleting Xist in ES cells precludes PRC2 recruitment during differentiation and conditionally deleting Xist in MEF cells results in loss of PRC2 on Xi. However, the kinetics with which PRC2 is recruited to and lost from X are not known. Because Xist RNA directly recruits PRC2, it was asked whether LNA molecule-mediated displacement of Xist results in immediate loss of PRC2 by immunostaining for Ezh2 in MEFs after LNA molecule delivery. Upon treatment with the Repeat C LNA molecules, Ezh2 was rapidly lost. There was nearly perfect concordance between Xist and PRC2 loss. At 1 and 3 hr, Ezh2 foci were never observed in nuclei that had lost Xist and, conversely, were always observed in nuclei with restored Xist clouds. The loss of Ezh2 on Xi was due to Ezh2 protein turnover. Transient displacement of PRC2, however, does not lead to appreciable H3K27me3 loss within the 1-8 hr timeframe. Thus, PRC2's localization onto Xi absolutely depends on Xist RNA for both initial targeting and for stable association after XCI is established, but the H3K27me3 mark is stable in the short term when Xist and PRC2 are displaced.

Given this, it was asked whether LNA molecules affected gene silencing. At 3 hr when Xist was maximally displaced, RNA FISH was performed for Xist and either Pgkl or Hprt, two X-linked genes subject to XCI. In control-nucleofected (LNA-Scr) cells, Xist clouds were observed from Xi and nascent Pgkl or Hprt transcripts from Xa. Nucleofection with LNA-C1 and LNA-4978 did not change the expression pattern, as two foci of Pgkl transcripts were still seen in 79% (n=39) of controls and 80% (n=36) of LNA-C1-treated cells, and two foci of Hprt RNA were seen in 84% (n=44) of controls and 79% (n=35) of LNA-C1-treated cells. Four foci of Pgkl or Hprt transcripts were never seen. Thus, consistent with retention of H3K27me3, silencing was not disrupted by transient loss of Xist and PRC2.

Example 10 A Broader Domain Around Repeat C is Required for Xist Localization

The next experiments investigated other conserved repeats within Xist. As Repeat A has already been shown to be essential for targeting PRC2, the experiments focused on Repeats B, E, and F, and found tht Xist localization was not affected by targeting any repeat individually or in combination. Conserved unique regions of Xist were also tested, including LNA-726, LNA-4978 and LNA-5205, and LNA-3′ (distal terminus of Xist). None affected Xist localization except for LNA-4978, which corresponds to a 15-nt element located 280 bp downstream of Repeat C. LNA-4978 induced effects similar to LNA-C1/C2 but differed by its slower kinetics. At 1 hr, Xist clouds were still visible but appeared faint and dispersed (78%, n=125). The number of clouds reached a minimum at 3 hr (25%, n=158). At 8 hr, Xist was visible as small pinpoints (39%, n=123). Recovery was not complete until the 24-hr timepoint. As for Repeat C LNA molecules, loss of Xist was not due to RNA turnover, as determined by qRT-PCR, and Ezh2 was displaced without affecting H3K27me3 or change in Ezh2 protein level. Therefore, Xist localization to chromatin involves a broader region encompass both Repeat C and a unique region directly downstream of the repeat.

To determine if the two motifs cooperate, LNA-4978 and LNA-C1 were nucleofected separately or together into MEFs. As expected, treating with LNA-C1 alone resulted in loss of Xist RNA clouds by 1 hr and recovery beginning at 3 hr, and treating with LNA-4978 showed loss and recovery at 3 hr and 8 hr, respectively. Treating with both LNA molecules expanded the window of Xist depletion: Loss of Xist RNA and Ezh2 was observed by 1 hr (as was the case for LNA-C1 alone) and recovery did not begin until the 8 hr timepoint (as was the case for LNA-4978 alone). Thus, the LNA molecule effects were additive, not synergistic, as the effects were not enhanced beyond the widening of the Xist-depleted time window.

Example 11 Ezh2 Recovery after LNA Molecule Nucleofection is Slow but Uniform Along Xi

Finally, it was asked whether Ezh2 retargeting to Xi closely follows the piecemeal relocalization of Xist RNA during the recovery phase. Because PRC2 generally binds near promoters, Ezh2 localization at X-gene promoters was analyzed by quantitative chromatin immunoprecipitation (qChIP). Although female cells have two Xs and Ezh2 epitopes pulled down by the antibody could theoretically come from either Xa or Xi, evidence indicates that the vast bulk of Ezh2 and H3K27me3 is bound to Xi. Ezh2 was indeed enriched at promoters of genes that are silenced on Xi (e.g., Xmr, Pgkl), but not at promoters of genes (e.g., Jaridlc) that escape XCI. Then, MEF cells were nucleofected with LNA-C1 and performed qChIP using anti-Ezh2 antibodies between 1 and 24 hr. At t=1 hr, Ezh2 levels decreased dramatically at all tested target gene promoters to background levels, indicating that depletion of promoter-bound Ezh2 closely followed Xist displacement along Xi. At the 3- and 8-hr points, there was a gradual, uniform increase in Ezh2 levels across all genes, with many genes appearing to have reached saturating amounts of Ezh2 by t=8 hr. On promoters with the highest levels of Ezh2 at t=0 hr, Ezh2 levels did not fully recover until 24 hr. Thus, ChIP pulldowns were expected to originate predominantly, if not nearly exclusively, from Xi. In contrast, Ezh2 levels at the En1 control, a known autosomal PRC2 target, did not change significantly. Thus, Ezh2 levels fall and rise with similar kinetics throughout Xi. The loss of Xist RNA and Ezh2 binding between 1 and 8 hrs presents a window of opportunity during which cells could be reprogrammed to achieve novel epigenetic states.

TABLE 3 Hexamers that are not seed sequences of human miRNAs AAAAAA, AAAAAG, AAAACA, AAAAGA, AAAAGC, AAAAGG, AAAAUA, AAACAA, AAACAC, AAACAG, AAACAU, AAACCC, AAACCU, AAACGA, AAACGC, AAACGU, AAACUA, AAACUC, AAACUU, AAAGAU, AAAGCC, AAAGGA, AAAGGG, AAAGUC, AAAUAC, AAAUAU, AAAUCG, AAAUCU, AAAUGC, AAAUGU, AAAUUA, AAAUUG, AACAAC, AACAAG, AACAAU, AACACA, AACACG, AACAGA, AACAGC, AACAGG, AACAUC, AACAUG, AACCAA, AACCAC, AACCAG, AACCAU, AACCCC, AACCCG, AACCGA, AACCGC, AACCGG, AACCUA, AACCUU, AACGAA, AACGAC, AACGAG, AACGAU, AACGCU, AACGGG, AACGGU, AACGUA, AACGUC, AACGUG, AACGUU, AACUAU, AACUCA, AACUCC, AACUCG, AACUGA, AACUGC, AACUGU, AACUUA, AACUUC, AACUUG, AACUUU, AAGAAA, AAGAAG, AAGAAU, AAGACG, AAGAGA, AAGAGC, AAGAGG, AAGAGU, AAGAUU, AAGCAA, AAGCAC, AAGCAG, AAGCAU, AAGCCA, AAGCCC, AAGCCG, AAGCCU, AAGCGA, AAGCGG, AAGCGU, AAGCUA, AAGGAA, AAGGAC, AAGGCU, AAGGGC, AAGGGU, AAGGUU, AAGUAA, AAGUAC, AAGUAU, AAGUCC, AAGUCG, AAGUGA, AAGUGG, AAGUUA, AAGUUU, AAUAAA, AAUAAC, AAUAAG, AAUAAU, AAUACA, AAUACC, AAUACG, AAUAGA, AAUAGC, AAUAGG, AAUAGU, AAUAUC, AAUAUU, AAUCAA, AAUCAU, AAUCCA, AAUCCC, AAUCCG, AAUCGA, AAUCGC, AAUCGU, AAUCUA, AAUCUG, AAUCUU, AAUGAA, AAUGAC, AAUGAG, AAUGAU, AAUGCG, AAUGCU, AAUGGA, AAUGGU, AAUGUA, AAUGUC, AAUGUG, AAUUAA, AAUUAC, AAUUAG, AAUUCC, AAUUCG, AAUUGA, AAUUGG, AAUUGU, AAUUUC, AAUUUG, ACAAAA, ACAAAC, ACAAAG, ACAAAU, ACAACC, ACAACG, ACAACU, ACAAGA, ACAAGC, ACAAGU, ACAAUC, ACAAUG, ACAAUU, ACACAG, ACACCA, ACACCC, ACACCG, ACACCU, ACACGA, ACACGC, ACACGU, ACACUC, ACACUG, ACACUU, ACAGAA, ACAGAC, ACAGCC, ACAGCG, ACAGCU, ACAGGG, ACAGUC, ACAGUG, ACAGUU, ACAUAA, ACAUAC, ACAUCC, ACAUCG, ACAUCU, ACAUGA, ACAUGC, ACAUGU, ACAUUG, ACAUUU, ACCAAA, ACCAAC, ACCAAG, ACCAAU, ACCACC, ACCACG, ACCAGA, ACCAGU, ACCAUA, ACCAUG, ACCAUU, ACCCAA, ACCCAC, ACCCCA, ACCCCG, ACCCGA, ACCCGC, ACCCUA, ACCCUC, ACCCUU, ACCGAA, ACCGAC, ACCGAU, ACCGCA, ACCGCC, ACCGCG, ACCGCU, ACCGGA, ACCGGC, ACCGGU, ACCGUA, ACCGUC, ACCGUG, ACCGUU, ACCUAA, ACCUAC, ACCUAG, ACCUAU, ACCUCA, ACCUCC, ACCUCG, ACCUCU, ACCUGA, ACCUGC, ACCUGU, ACCUUA, ACCUUC, ACCUUU, ACGAAA, ACGAAC, ACGAAG, ACGAAU, ACGACA, ACGACC, ACGACG, ACGACU, ACGAGA, ACGAGC, ACGAGG, ACGAGU, ACGAUA, ACGAUC, ACGAUG, ACGAUU, ACGCAA, ACGCAG, ACGCAU, ACGCCC, ACGCCG, ACGCCU, ACGCGA, ACGCGG, ACGCGU, ACGCUA, ACGCUG, ACGCUU, ACGGAA, ACGGAC, ACGGAG, ACGGAU, ACGGCC, ACGGCG, ACGGCU, ACGGGC, ACGGGG, ACGGGU, ACGGUA, ACGGUC, ACGGUG, ACGGUU, ACGUAA, ACGUAC, ACGUAU, ACGUCC, ACGUCG, ACGUCU, ACGUGA, ACGUGC, ACGUGG, ACGUGU, ACGUUA, ACGUUC, ACGUUG, ACGUUU, ACUAAA, ACUAAG, ACUAAU, ACUACA, ACUACC, ACUACG, ACUACU, ACUAGG, ACUAUC, ACUAUG, ACUAUU, ACUCAU, ACUCCC, ACUCCG, ACUCCU, ACUCGA, ACUCGC, ACUCGG, ACUCUC, ACUCUU, ACUGAG, ACUGAU, ACUGCC, ACUGCG, ACUGCU, ACUGGG, ACUGGU, ACUGUC, ACUUAA, ACUUAC, ACUUAU, ACUUCA, ACUUCC, ACUUCG, ACUUCU, ACUUGA, ACUUGC, ACUUGU, ACUUUA, ACUUUC, ACUUUG, AGAAAA, AGAAAC, AGAAAG, AGAACC, AGAACG, AGAACU, AGAAGC, AGAAGU, AGAAUA, AGAAUC, AGAAUG, AGAAUU, AGACAA, AGACAC, AGACAU, AGACCA, AGACCC, AGACCG, AGACCU, AGACGA, AGACGC, AGACGU, AGACUA, AGACUC, AGACUU, AGAGAC, AGAGAG, AGAGAU, AGAGCC, AGAGCG, AGAGCU, AGAGGC, AGAGGG, AGAGGU, AGAGUA, AGAGUU, AGAUAC, AGAUAG, AGAUAU, AGAUCC, AGAUCG, AGAUCU, AGAUGA, AGAUGC, AGAUGG, AGAUUA, AGAUUC, AGAUUG, AGAUUU, AGCAAC, AGCACA, AGCACG, AGCACU, AGCAGA, AGCAUA, AGCAUC, AGCAUG, AGCCAA, AGCCAU, AGCCCA, AGCCGA, AGCCGC, AGCCGG, AGCCGU, AGCCUA, AGCCUC, AGCGAA, AGCGAG, AGCGAU, AGCGCA, AGCGCC, AGCGCG, AGCGCU, AGCGGA, AGCGGC, AGCGGU, AGCGUA, AGCGUC, AGCGUG, AGCGUU, AGCUAA, AGCUAC, AGCUAG, AGCUAU, AGCUCA, AGCUCC, AGCUCG, AGCUCU, AGCUGA, AGCUGG, AGCUGU, AGCUUC, AGCUUU, AGGAAU, AGGACC, AGGACG, AGGAGA, AGGAGU, AGGAUA, AGGCAA, AGGCAU, AGGCCG, AGGCGA, AGGCGC, AGGCGG, AGGCUA, AGGCUC, AGGCUU, AGGGAC, AGGGAU, AGGGGA, AGGGGU, AGGGUA, AGGGUG, AGGUAA, AGGUAC, AGGUCA, AGGUCC, AGGUCU, AGGUGA, AGGUGC, AGGUGG, AGGUGU, AGGUUC, AGGUUG, AGUAAA, AGUAAG, AGUAAU, AGUACA, AGUACG, AGUAGC, AGUAGG, AGUAUA, AGUAUC, AGUAUG, AGUAUU, AGUCAA, AGUCAC, AGUCAG, AGUCAU, AGUCCA, AGUCCG, AGUCCU, AGUCGA, AGUCGC, AGUCGG, AGUCGU, AGUCUA, AGUCUC, AGUCUG, AGUCUU, AGUGAA, AGUGAC, AGUGCG, AGUGGG, AGUGUC, AGUUAA, AGUUAC, AGUUAG, AGUUCC, AGUUCG, AGUUGA, AGUUGC, AGUUGU, AGUUUA, AGUUUC, AGUUUG, AGUUUU, AUAAAC, AUAAAU, AUAACA, AUAACC, AUAACG, AUAACU, AUAAGA, AUAAGC, AUAAGG, AUAAGU, AUAAUC, AUAAUG, AUAAUU, AUACAC, AUACAG, AUACAU, AUACCA, AUACCC, AUACCG, AUACGA, AUACGC, AUACGG, AUACGU, AUACUA, AUACUC, AUACUG, AUACUU, AUAGAA, AUAGAC, AUAGAU, AUAGCA, AUAGCG, AUAGCU, AUAGGA, AUAGGU, AUAGUA, AUAGUC, AUAGUG, AUAGUU, AUAUAC, AUAUAG, AUAUCC, AUAUCG, AUAUCU, AUAUGA, AUAUGC, AUAUGG, AUAUGU, AUAUUC, AUAUUG, AUAUUU, AUCAAA, AUCAAC, AUCAAG, AUCAAU, AUCACA, AUCACC, AUCACG, AUCAGC, AUCAGG, AUCCAA, AUCCAU, AUCCCC, AUCCCG, AUCCGA, AUCCGC, AUCCGG, AUCCUA, AUCCUC, AUCCUG, AUCGAA, AUCGAC, AUCGAG, AUCGAU, AUCGCA, AUCGCC, AUCGCG, AUCGCU, AUCGGC, AUCGGG, AUCGGU, AUCGUC, AUCGUG, AUCGUU, AUCUAA, AUCUAC, AUCUAG, AUCUAU, AUCUCC, AUCUCG, AUCUGU, AUCUUG, AUCUUU, AUGAAA, AUGAAC, AUGAAG, AUGAAU, AUGACC, AUGACU, AUGAGG, AUGAGU, AUGAUA, AUGAUC, AUGAUU, AUGCAA, AUGCAG, AUGCCA, AUGCCC, AUGCCG, AUGCGA, AUGCGG, AUGCGU, AUGCUC, AUGCUU, AUGGAC, AUGGCC, AUGGGA, AUGGGC, AUGGGU, AUGGUC, AUGGUG, AUGUAC, AUGUAU, AUGUCA, AUGUCC, AUGUCG, AUGUGU, AUGUUA, AUGUUC, AUUAAA, AUUAAC, AUUAAG, AUUAAU, AUUACA, AUUACC, AUUACG, AUUACU, AUUAGA, AUUAGC, AUUAGG, AUUAGU, AUUAUA, AUUAUC, AUUAUG, AUUCAC, AUUCCA, AUUCCG, AUUCCU, AUUCGA, AUUCGC, AUUCGG, AUUCGU, AUUCUA, AUUCUC, AUUCUU, AUUGAA, AUUGAC, AUUGAU, AUUGCC, AUUGCG, AUUGCU, AUUGGA, AUUGGC, AUUGGG, AUUGGU, AUUGUA, AUUGUC, AUUGUG, AUUGUU, AUUUAA, AUUUAG, AUUUAU, AUUUCC, AUUUCG, AUUUCU, AUUUGA, AUUUGC, AUUUGU, AUUUUA, AUUUUC, AUUUUG, AUUUUU, CAAAAG, CAAACA, CAAACC, CAAACG, CAAACU, CAAAGA, CAAAGG, CAAAUA, CAAAUU, CAACAC, CAACAU, CAACCA, CAACCC, CAACCG, CAACGA, CAACGC, CAACGG, CAACGU, CAACUA, CAACUC, CAACUG, CAACUU, CAAGAA, CAAGAC, CAAGAU, CAAGCA, CAAGCC, CAAGCG, CAAGCU, CAAGGA, CAAGGG, CAAGUC, CAAGUG, CAAGUU, CAAUAA, CAAUAC, CAAUAG, CAAUCC, CAAUCG, CAAUCU, CAAUGA, CAAUGC, CAAUGG, CAAUGU, CAAUUC, CAAUUG, CAAUUU, CACAAU, CACACA, CACACG, CACACU, CACAGA, CACAGC, CACAGG, CACAUA, CACAUC, CACAUU, CACCAA, CACCAC, CACCAU, CACCCA, CACCCC, CACCCG, CACCGA, CACCGC, CACCGG, CACCGU, CACCUA, CACCUU, CACGAA, CACGAC, CACGAG, CACGAU, CACGCA, CACGCC, CACGCU, CACGGA, CACGGC, CACGGG, CACGGU, CACGUA, CACGUC, CACGUG, CACGUU, CACUAA, CACUAG, CACUAU, CACUCA, CACUCG, CACUGA, CACUGC, CACUGG, CACUUA, CACUUC, CACUUU, CAGAAA, CAGAAG, CAGAAU, CAGACC, CAGACG, CAGAGC, CAGAUA, CAGAUC, CAGCCG, CAGCCU, CAGCGA, CAGCGC, CAGCGG, CAGCGU, CAGCUC, CAGCUU, CAGGAU, CAGGGG, CAGGGU, CAGGUA, CAGGUC, CAGGUU, CAGUAC, CAGUCG, CAGUUG, CAUAAA, CAUAAC, CAUAAG, CAUAAU, CAUACA, CAUACC, CAUACG, CAUACU, CAUAGA, CAUAGG, CAUAGU, CAUAUA, CAUAUC, CAUAUG, CAUCAA, CAUCAC, CAUCAG, CAUCAU, CAUCCA, CAUCCC, CAUCCG, CAUCGA, CAUCGC, CAUCGG, CAUCGU, CAUCUA, CAUCUC, CAUCUG, CAUCUU, CAUGAA, CAUGAC, CAUGAG, CAUGAU, CAUGCA, CAUGCC, CAUGCG, CAUGCU, CAUGGC, CAUGGG, CAUGGU, CAUGUA, CAUGUC, CAUGUU, CAUUAA, CAUUAC, CAUUAG, CAUUCA, CAUUCC, CAUUCG, CAUUCU, CAUUGA, CAUUGG, CAUUUC, CAUUUG, CAUUUU, CCAAAA, CCAAAC, CCAAAG, CCAAAU, CCAACA, CCAACC, CCAACG, CCAACU, CCAAGA, CCAAGC, CCAAGG, CCAAUC, CCAAUG, CCAAUU, CCACAA, CCACAC, CCACAG, CCACAU, CCACCA, CCACCC, CCACCG, CCACCU, CCACGA, CCACGC, CCACGG, CCACGU, CCACUA, CCACUC, CCACUU, CCAGAA, CCAGAC, CCAGAG, CCAGCC, CCAGGU, CCAGUC, CCAGUU, CCAUAA, CCAUAC, CCAUAG, CCAUAU, CCAUCA, CCAUCC, CCAUCU, CCAUGA, CCAUGC, CCAUGG, CCAUUC, CCAUUG, CCAUUU, CCCAAC, CCCAAG, CCCAAU, CCCACA, CCCAGA, CCCAGC, CCCAGU, CCCAUA, CCCAUC, CCCAUG, CCCAUU, CCCCAA, CCCCAG, CCCCAU, CCCCCC, CCCCCG, CCCCCU, CCCCGA, CCCCGC, CCCCGU, CCCCUA, CCCCUC, CCCGAA, CCCGAC, CCCGAU, CCCGCA, CCCGCU, CCCGGA, CCCGGC, CCCGUA, CCCGUG, CCCGUU, CCCUAA, CCCUAG, CCCUCA, CCCUCU, CCCUGC, CCCUUA, CCCUUC, CCCUUU, CCGAAA, CCGAAC, CCGAAU, CCGACA, CCGACC, CCGACG, CCGACU, CCGAGA, CCGAGG, CCGAGU, CCGAUA, CCGAUC, CCGAUG, CCGAUU, CCGCAA, CCGCAC, CCGCAG, CCGCAU, CCGCCA, CCGCCC, CCGCCG, CCGCCU, CCGCGA, CCGCGC, CCGCGG, CCGCGU, CCGCUA, CCGCUC, CCGCUG, CCGCUU, CCGGAA, CCGGAU, CCGGCA, CCGGCC, CCGGCG, CCGGCU, CCGGGA, CCGGGC, CCGGGG, CCGGGU, CCGGUA, CCGGUC, CCGGUG, CCGUAA, CCGUAG, CCGUAU, CCGUCA, CCGUCC, CCGUCG, CCGUGA, CCGUGU, CCGUUA, CCGUUC, CCGUUG, CCGUUU, CCUAAC, CCUAAG, CCUAAU, CCUACA, CCUACC, CCUACG, CCUACU, CCUAGA, CCUAGC, CCUAGG, CCUAGU, CCUAUA, CCUAUC, CCUAUG, CCUAUU, CCUCAA, CCUCAC, CCUCAG, CCUCAU, CCUCCA, CCUCCC, CCUCCG, CCUCGA, CCUCGC, CCUCGG, CCUCGU, CCUCUA, CCUCUG, CCUGAC, CCUGAU, CCUGCA, CCUGGG, CCUGGU, CCUGUU, CCUUAA, CCUUAC, CCUUAG, CCUUAU, CCUUCG, CCUUGA, CCUUGU, CCUUUA, CCUUUC, CCUUUU, CGAAAA, CGAAAC, CGAAAG, CGAAAU, CGAACA, CGAACC, CGAACG, CGAACU, CGAAGA, CGAAGC, CGAAGG, CGAAGU, CGAAUA, CGAAUC, CGAAUG, CGAAUU, CGACAA, CGACAC, CGACAU, CGACCA, CGACCU, CGACGA, CGACGC, CGACGG, CGACGU, CGACUA, CGACUG, CGACUU, CGAGAA, CGAGAC, CGAGAG, CGAGAU, CGAGCA, CGAGCC, CGAGCG, CGAGCU, CGAGGC, CGAGGG, CGAGGU, CGAGUA, CGAGUC, CGAGUG, CGAGUU, CGAUAA, CGAUAC, CGAUAG, CGAUAU, CGAUCA, CGAUCC, CGAUCG, CGAUCU, CGAUGA, CGAUGC, CGAUGG, CGAUGU, CGAUUA, CGAUUC, CGAUUG, CGAUUU, CGCAAA, CGCAAC, CGCAAG, CGCAAU, CGCACA, CGCACC, CGCACG, CGCAGA, CGCAGC, CGCAGG, CGCAGU, CGCAUA, CGCAUC, CGCAUG, CGCAUU, CGCCAA, CGCCAC, CGCCAG, CGCCAU, CGCCCA, CGCCCC, CGCCCG, CGCCGA, CGCCGC, CGCCGG, CGCCGU, CGCCUA, CGCCUG, CGCCUU, CGCGAA, CGCGAC, CGCGAG, CGCGAU, CGCGCA, CGCGCC, CGCGCG, CGCGCU, CGCGGA, CGCGGC, CGCGGG, CGCGGU, CGCGUA, CGCGUC, CGCGUG, CGCGUU, CGCUAA, CGCUAC, CGCUAG, CGCUAU, CGCUCA, CGCUCC, CGCUCG, CGCUCU, CGCUGA, CGCUGC, CGCUGG, CGCUGU, CGCUUA, CGCUUC, CGCUUG, CGGAAA, CGGAAC, CGGAAG, CGGACA, CGGACC, CGGACG, CGGACU, CGGAGC, CGGAGG, CGGAGU, CGGAUA, CGGAUU, CGGCAA, CGGCAC, CGGCAG, CGGCCA, CGGCCC, CGGCCG, CGGCGC, CGGCGG, CGGCGU, CGGCUA, CGGCUC, CGGCUG, CGGCUU, CGGGAA, CGGGAC, CGGGAG, CGGGAU, CGGGCA, CGGGCC, CGGGCG, CGGGCU, CGGGGU, CGGGUA, CGGGUC, CGGGUG, CGGUAA, CGGUAC, CGGUAG, CGGUAU, CGGUCA, CGGUCG, CGGUCU, CGGUGA, CGGUGG, CGGUGU, CGGUUA, CGGUUC, CGGUUG, CGGUUU, CGUAAA, CGUAAC, CGUAAG, CGUAAU, CGUACA, CGUACG, CGUACU, CGUAGA, CGUAGC, CGUAGG, CGUAGU, CGUAUA, CGUAUC, CGUAUG, CGUAUU, 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UCUUCA, UCUUCC, UCUUCG, UCUUCU, UCUUGC, UCUUGG, UCUUGU, UCUUUA, UCUUUC, UCUUUG, UCUUUU, UGAAAA, UGAAAC, UGAACA, UGAACC, UGAAGG, UGAAUC, UGAAUG, UGACAA, UGACAC, UGACAG, UGACCA, UGACCC, UGACCG, UGACGA, UGACGC, UGACGG, UGACGU, UGACUA, UGACUC, UGACUU, UGAGAG, UGAGAU, UGAGCA, UGAGCC, UGAGCU, UGAGGC, UGAGGU, UGAGUA, UGAGUU, UGAUAC, UGAUAG, UGAUAU, UGAUCA, UGAUCG, UGAUCU, UGAUGA, UGAUGC, UGAUGG, UGAUGU, UGAUUA, UGAUUC, UGAUUG, UGAUUU, UGCAAC, UGCAAG, UGCACA, UGCACG, UGCAGG, UGCAGU, UGCAUC, UGCCCA, UGCCCC, UGCCCG, UGCCGA, UGCCGC, UGCCGG, UGCCGU, UGCCUA, UGCCUC, UGCCUG, UGCCUU, UGCGAA, UGCGAC, UGCGAU, UGCGCC, UGCGCG, UGCGCU, UGCGGC, UGCGGG, UGCGGU, UGCGUA, UGCGUC, UGCGUG, UGCGUU, UGCUAC, UGCUAU, UGCUCC, UGCUCG, UGCUGC, UGCUGG, UGCUGU, UGCUUA, UGCUUU, UGGAAC, UGGAAG, UGGAGC, UGGAUC, UGGAUU, UGGCAA, UGGCAC, UGGCAG, UGGCCG, UGGCCU, UGGCGA, UGGCGC, UGGCGU, UGGCUA, UGGCUC, UGGCUU, UGGGAA, UGGGCA, UGGGCC, UGGGGC, UGGGUC, UGGUAA, UGGUAG, UGGUAU, UGGUCC, UGGUCG, UGGUCU, UGGUGA, UGGUGC, UGGUGG, UGGUGU, UGGUUA, UGGUUG, UGUAAA, UGUAAC, UGUAAG, UGUACC, UGUACG, UGUACU, UGUAGA, UGUAGC, UGUAGU, UGUAUC, UGUAUU, UGUCAA, UGUCAC, UGUCAG, UGUCAU, UGUCCA, UGUCCC, UGUCCG, UGUCGA, UGUCGC, UGUCGG, UGUCGU, UGUCUA, UGUCUC, UGUGAC, UGUGAG, UGUGAU, UGUGCA, UGUGGU, UGUGUA, UGUGUU, UGUUAC, UGUUAG, UGUUAU, UGUUCA, UGUUCC, UGUUCG, UGUUGG, UGUUGU, UGUUUA, UGUUUC, UGUUUG, UGUUUU, UUAAAA, UUAAAC, UUAAAG, UUAAAU, UUAACC, UUAACG, UUAACU, UUAAGU, UUAAUA, UUAAUC, UUAAUG, UUAAUU, UUACAA, UUACAC, UUACAG, UUACAU, UUACCA, UUACCC, UUACCG, UUACCU, UUACGA, UUACGC, UUACGG, UUACGU, UUACUA, UUACUC, UUACUG, UUACUU, UUAGAA, UUAGAC, UUAGCC, UUAGCG, UUAGCU, UUAGGC, UUAGGU, UUAGUA, UUAGUC, UUAGUU, UUAUAA, UUAUAC, UUAUAG, UUAUAU, UUAUCC, UUAUCG, UUAUCU, UUAUGA, UUAUGG, UUAUGU, UUAUUA, UUAUUC, UUAUUG, UUAUUU, UUCAAC, UUCAAU, UUCACA, UUCACC, UUCACG, UUCACU, UUCAGC, UUCAGG, UUCAGU, UUCAUA, UUCAUC, UUCAUG, UUCAUU, UUCCAA, UUCCCA, UUCCCG, UUCCGA, UUCCGU, UUCCUU, UUCGAA, UUCGAC, UUCGAG, UUCGAU, UUCGCA, UUCGCC, UUCGCG, UUCGCU, UUCGGA, UUCGGC, UUCGGG, UUCGGU, UUCGUA, UUCGUC, UUCGUG, UUCGUU, UUCUAC, UUCUAG, UUCUCA, UUCUCG, UUCUGG, UUCUUA, UUCUUU, UUGAAA, UUGAAC, UUGAAG, UUGAAU, UUGACC, UUGACG, UUGACU, UUGAGA, UUGAGC, UUGAGU, UUGAUA, UUGAUC, UUGAUG, UUGAUU, UUGCAA, UUGCAC, UUGCAG, UUGCAU, UUGCCC, UUGCCG, UUGCGA, UUGCGC, UUGCGG, UUGCGU, UUGCUA, UUGCUC, UUGCUG, UUGCUU, UUGGAA, UUGGAG, UUGGCC, UUGGCG, UUGGCU, UUGGGC, UUGGGU, UUGGUA, UUGGUG, UUGUAA, UUGUAC, UUGUCA, UUGUCG, UUGUCU, UUGUGC, UUGUGG, UUGUUA, UUGUUG, UUGUUU, UUUAAA, UUUAAC, UUUAAG, UUUAAU, UUUACA, UUUACC, UUUACG, UUUACU, UUUAGA, UUUAGC, UUUAGG, UUUAGU, UUUAUA, UUUAUC, UUUAUG, UUUAUU, UUUCAU, UUUCCA, UUUCCG, UUUCCU, UUUCGA, UUUCGC, UUUCGG, UUUCGU, UUUCUA, UUUCUC, UUUCUG, UUUCUU, UUUGAA, UUUGAC, UUUGAG, UUUGAU, UUUGCC, UUUGCU, UUUGGA, UUUGGC, UUUGGG, UUUGGU, UUUGUA, UUUGUC, UUUGUU, UUUUAA, UUUUAG, UUUUAU, UUUUCC, UUUUCG, UUUUCU, UUUUGA, UUUUGC, UUUUGG, UUUUGU, UUUUUA, UUUUUC, UUUUUU

TABLE 2 Imprinted regions hit by the expanded PRC2 transcriptome. human liftOver Imprinted gene mm9 coordinates targeted by coordinates and (hg19) and PRC2-binding chromosome chromosome transcript and strand of PRC2- MGI human strand of PRC2- chromosome binding gene name for binding strand transcript Sequence mouse refGene transcript Sequence Wt1 (22431)+ chr2: 104956685− B934762 WT1(7490)− chr11: 32400584− B934864 105023768+ 32466719− Wt1 (22431)+ chr2: B934763 WT1(7490)− chr11: 32400584− B934865 104956685− 32466719+ 105023768− Gatm(67092)− chr2: 122410207− B934764 GATM(2628)− chr15: 45644412− B934866 122446997+ 45685240+ Gatm(67092)− chr2: 122410207− B934765 GATM(2628)− chr15: 45644412− B934867 122446997− 45685240− L3mbt1 (241764)+ chr2: 162759200− B934766 chr20: 42088449− B934868 162810257+ 42184934+ L3mbtI(241764)+ chr2: 162759200− B934767 chr20: 42088449− B934869 162810257− 42184934− Gnai3(14679)− chr3: 107900216− B934768 GNAI3(2773)+ chr1: 110081495− B934870 107959031+ 110150201− Gnai3(14679)− chr3: 107900216− B934769 GNAI3(2773)+ chr1: 110081495− B934871 107959031− 110150201+ Mkrn 1(54484)− chr5: 89257179− B934770 MKRN chr7: 140155983− B934905 89278370+ 1(23608)− 140179369+ Mkrn 1(54484)− chr5: 89257179− B934771 MKRN chr7: 140155983− B934906 89278370− 1(23608)− 140179369− Calcr(12311)− chr6: 3625733− B934772 CALCR(799)− chr7: 93050410− B934872 3728615+ 93230834+ Calcr(12311)− chr6: 3625733− B934773 CALCR(799)− chr7: 93050410− B934873 3728615− 93230834− Tfpi2(21789)− chr6: 3902594− B934774 TFP 12(7980)− chr7: 93490853− B934874 3928353+ 93527640+ Tfpi2(21789)− chr6: 3902594− B934775 TFP 12(7980)− chr7: 93490853− B934875 3928353− 93527640− Sgce(20392)− chr6: 4614349− B934776 SGCE(8910)− chr7: 94211984− B934876 4707098− 94294870− Peg 10(170676)+ chr6: 4687379− B934777 PEG10(23089)+ chr7: 94275257− B934877 4720475− 94299422− Ppplr9a(243725)+ chr6: 4843319− B934778 PPP1R9A(55607)+ chr7: 94528605− B934878 5125660+ 94935514+ Ppplr9a(243725)+ chr6: 4843319− B934779 PPP1R9A(55607)+ chr7: 94528605− B934879 5125660− 94935514− Pon1 (18979)− chr6: 5108104− B934780 PON1(5444)− chr7: 94917863− B934880 5153823+ 94958087+ Pon1 (18979)− chr6: 5108104− B934781 PON 1(5444)− chr7: 94917863− B934881 5153823− 94958087− Pon3(269823)− chr6: 5160851− B934782 PON3(5446)− chr7: 94989184− B934907 5216232+ 95025687+ Pon2(330260)− chr6: 5204623− B934783 PON2(5445)− chr7: 95034174− B934908 5258372+ 95064384+ Pon2(330260)− chr6: 5204623− B934784 PON2(5445)− chr7: 95034174− B934909 5258372− 95064384− Asb4(65255)+ chr6: 5323385− B934785 ASB4(51666)+ chr7: 95094541− B934882 5393021+ 95179369+ Asb4(65255)+ chr6: 5323385− B934786 ASB4(51666)+ chr7: 95094541− B934883 5393021− 95179369− Cpa4(71791)+ chr6: 30508375− B934787 CPA4(51200)+ chr7: 129922767− B934884 30551746+ 129974483+ Cpa4(71791)+ chr6: 30508375− B934788 CPA4(51200)+ chr7: 129922767− B934885 30551746− 129974483− Nap115(58243)− chr6: 58845227− B934789 NAP1L5(266812)− chr4: 89617066− B934910 58867058+ 89619023+ Nap115(58243)− chr6: 58845227− B934790 NAP1L5(266812)− chr4: 89617066− B934911 58867058− 89619023− Zim2(76637)− chr7: 6594458− B934791 ZIM2(23619)− chr19: 57285923− B934912 6625116+ 57352097+ Zim2(76637)− chr7: 6594458− B934792 ZIM2(23619)− chr19: 57285923− B934913 6625116− 57352097− Zim1(22776)− chr7: 6618153− B934793 6659142+ Zim1(22776)− chr7: 6618153− B934794 6659142− Peg3(18616)− chr7: 6648670− B934795 PEG3(5178)− chr19: 57319764− B934886 6693129+ 57358664+ Peg3(18616)− chr7: 6648670− B934796 PEG3(5178)− chr19: 57319764− B934887 6693129− 57358664− Usp29(57775)+ chr7: 6673293− B934797 USP29(57663)+ chr19: 57631509− B629991 6929926+ 57643293+ Usp29(57775)+ chr7: 6673293− B934798 USP29(57663)+ chr19: 57631509− B629992 6929926− 57643293− Gabrg3(14407)− chr7: 63969611− B934799 GABRG3(2567)+ chr15: 27216429− B630983 64652167+ 27778373− Gabrg3(14407)− chr7: 63969611− B934800 GABRG3(2567)+ chr15: 27216429− 64652167− 27778373+ Gabra5(110886)− chr7: 64653038− B934801 GABRAS(2558)+ chr15: 27111866− B934914 64775378+ 27194357− Gabra5(110886)− chr7: 64653038− B934802 GABRAS(2558)+ chr15: 27111866− B934915 64775378− 27194357+ Gabrb3(14402)+ chr7: 64835903− B934803 GABRB3(2562)− chr15: 26788694− B934916 65094171+ 27018223− Gabrb3(14402)+ chr7: 64835903− B934804 GABRB3(2562)− chr15: 26788694− B934917 65094171− 27018223+ Atp10a(11982)+ chr7: 65903701− B934805 ATP10A(57194)− chr15: 25923860− B630990 66094160+ 26108349− Snord116/Pwcr1 chr7: 66921359− B934806 (64243)− 66941448+ Snord116/Pwcr1 chr7: 66921359− B934807 (64243)− 66941448− Snrpn(20646)− chr7: 67117999− B934808 SNRPN(6638)+ chr15: 25200135− B934918 67159989+ 25223729− Snrpn(20646)− chr7: 67117999− B934809 SNRPN(6638)+ chr15: 25200135− B934919 67159989− 25223729+ Snurf(84704)− chr7: 67123487− B934810 SNURF(8926)+ chr15: 25200135− B934918 67160009+ 25223729− Snurf(84704)− chr7: 67123487− B934811 SNURF(8926)+ chr15: 25200135− B934919 67160009− 25223729+ Ndn(17984)+ chr7: 69483233− B934812 NDN(4692)− chr15: 23915288− B934888 69504813− 23938997+ Mage12(27385)+ chr7: 69511864− B934813 MAGEL2(54551)− chr15: 23888696− B631003 69536525+ 23892993− Mage12(27385)+ chr7: 69511864− B934814 MAGEL2(54551)− chr15: 23888696− B631004 69536525− 23892993+ Mkrn3(22652)− chr7: 69552478− B934815 MKRN3(7681)+ chr15: 23810454− B934920 69575024+ 23813166− Mkrn3(22652)− chr7: 69552478− B934816 MKRN3(7681)+ chr15: 23810454− B934921 69575024− 23813166+ Peg12(27412)− chr7: 69596756− B934817 69619395+ Peg12(27412)− chr7: 69596756− B934818 69619395− Ins2(16334)− chr7: 149854565− B934819 INS(3630)− chr11: 2181009− B632396 149875612+ 2182439+ Ins2(16334)− chr7: 149854565− B934820 INS(3630)− chr11: 2181009− B632397 149875612− 2182439− Tspan32(27027)+ chr7: 150181595− B934821 TSPAN32(10077)+ chr11: 2323243− B632402 150215548+ 2339430+ Tspan32(27027)+ chr7: 150181595− B934822 TSPAN32(10077)+ chr11: 2323243− B632403 150215548− 2339430− S1c22a18(18400)+ chr7: 150649693− B934823 SLC22A18(5002)+ chr11: 2923512− B934922 150695226+ 2946476+ S1c22a18(18400)+ chr7: 150649693− B934824 SLC22A18(5002)+ chr11: 2923512− B934923 150695226− 2946476− PhIda2(22113)− chr7: 150677452− B934825 PHLDA2(7262)− chr11: 2949503− B934924 150698428+ 2950650+ PhIda2(22113)− chr7: 150677452− B934826 PHLDA2(7262)− chr11: 2949503− B934925 150698428− 2950650− Nap114(17955)− chr7: 150689483− B934827 NAP1L4(4676)− chr11: 2965660− B632419 150744994− 3013607− Tnfrsf23(79201)− chr7: 150841711− B934828 150881776− Osbp15(79196)− chr7: 150864666− B934829 OSBPL5(114879)− chr11: 3108346− B632422 150937867− 3186582− Sdhd(66925)− chr9: 50394450− B934830 SDHD(6392)+ chr11: 111957571− B634959 50421921+ 111966518− Rasgrf1(19417)+ chr9: 89794612− B934831 RASGRF1(5923)− chr15: 79252289− B934926 89934638+ 79383215− Rasgrf1(19417)+ chr9: 89794612− B934832 RASGRF1(5923)− chr15: 79252289− B934927 89934638− 79383215+ Plagl 1 (22634)+ chr10: 12800714− B934833 PLAGL1(5325)− chr6: 144257160− B934889 12859693+ 144341048− Ctnna3(216033)+ chr10: 62882845− B934834 CTNNA3(29119)− chr10: 67679725− B934928 64475689+ 69425416− Ctnna3(216033)+ chr10: 62882845− B934835 CTNNA3(29119)− chr10: 67679725− B934929 64475689− 69425416+ Dcn(13179)+ chr10: 96935000− B934836 DCN (1634)− chr12: 91539035− B934930 96990784− 91576806+ Ddc(13195)− chr11: 11704105− B934837 DDC(1644)− chr7: 50526134− B934931 11800403+ 50628768+ Grb10(14783)− chr11: 11820510− B934838 GRB10(2887)− chr7: 50657755− B934890 11947357+ 50871312+ Grb10(14783)− chr11: 11820510− B934839 GRB10(2887)− chr7: 50657755− 11947357− 50871312− Commd1(17846)− chr11: 22789727− B934840 COMMD1(150684)+ chr2: 62132803− B638303 22892283+ 62363205− Commd1(17846)− chr11: 22789727− B934841 COMMD150684)+ chr2: 62132803− B638304 22892283− 62363205+ U2af(22185)+ chr11: 22862036− B934842 22884907+ U2af(22185)+ chr11: 22862036− B934843 22884907− M1r337/Mirn337 chr12: 67749612− B934844 chr14: 47524741− B934892 (723843)+ 67769708+ 47544270+ M1r337/M1rn33 chr12: 67749612− B934845 chr14: 47524741− B934893 7(723843)+ 67769708− 47544270− DIk1 (13386)+ chr12: 110681432− B934846 OLK1(8788)+ chr14: 101183690− B934894 110708900+ 101211352+ Meg3/Gt12(17263)+ chr12: 110773827− B934847 chr14: 101287762− B934895 110809921− 101327347− 0103(107585)+ chr12: 111507442− B934848 0103(1735)+ chr14: 102013439− B934896 111529304+ 102036066+ Dio3(107585)+ chr12: 111507442− B934849 0103(1735)+ chr14: 102013439− B934897 111529304− 102036066− Htr2a(15558)+ chr14: 75030646− B934850 HTR2A(3356)− chr13: 47401097− B934898 75116665+ 47479311− Htr2a(15558)+ chr14: 75030646− B934851 HTR2A(3356)− chr13: 47401097− B934899 75116665− 47479311+ Kcnk9(223604)− chr15: 72335722− B934852 KCNK9(51305)− chr8: 140621242− B934900 72389882+ 140723023+ Peg13(353342)− chr15: 72626029− B934853 chr8: 141094733− B934901 72650753+ 141124284+ Peg13(353342)− chr15: 72626029− B934854 chr8: 141094733− B934902 72650753− 141124284− S1c38a4(69354)− chr15: 96815253− B934855 SLC38A4(55089)− chr12: 47116054− B934903 96896386+ 47237900+ S1c38a4(69354)− chr15: 96815253− B934856 SLC38A4(55089)− chr12: 47116054− B934904 96896386− 47237900− S1c22a3(20519)− chr17: 12602837− B934857 SLC22A3(6581)+ chr6: 160769425− B647595 12710569+ 160876014− SIc22a3(20519)− chr17: 12602837− B934858 SLC22A3(6581)+ chr6: 160769425− B647596 12710569− 160876014+ S1c22a2(20518)+ chr17: 12767054− B934859 SLC22A2(6582)− chr6: 160637794− B647597 12831353+ 160679963− Slc22a2(20518)+ chr17: 12767054− B934860 SLC22A2(6582)− chr6: 160637794− B647598 12831353− 160679963+ Igf2r(16004)− chr17: 12865278− B934861 IGF2R(3482)+ chr6: 160390131− B647601 12972529+ 160527583− Air/Airn(104103)+ chr17: 12931160− B934862 12954858+ Impact(16210)+ chr18: 13120760− B934863 IMPACT(55364)+ chr18: 22006609− B649028 13161456+ 22033494+

The foregoing written specification is considered to be sufficient to enable one skilled in the art to practice the invention. The present invention is not to be limited in scope by examples provided, since the examples are intended as a single illustration of one aspect of the invention and other functionally equivalent embodiments are within the scope of the invention. Various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and fall within the scope of the appended claims. The advantages and objects of the invention are not necessarily encompassed by each embodiment of the invention. 

1-30. (canceled)
 31. A single stranded oligonucleotide comprising a region of complementarity that is complementary with at least 8 consecutive nucleotides of a PRC2-associated region located in a first chromosome between 50 kilobases upstream of a 5′-end of a target gene and 50 kilobases downstream of a 3′-end of the target gene, wherein the oligonucleotide has at least one of: a) a sequence comprising 5′-X-Y-Z, wherein X is any nucleotide, Y is a nucleotide sequence of 6 nucleotides in length that is not a human seed sequence of a microRNA, and Z is a nucleotide sequence of 1 to 23 nucleotides in length; b) a sequence that does not comprise three or more consecutive guanosine nucleotides; c) a sequence that has less than a threshold level of sequence identity with every sequence of nucleotides, of equivalent length to the second nucleotide sequence, that are between 50 kilobases upstream of a 5′-end of an off-target gene and 50 kilobases downstream of a 3′-end of the off-target gene; d) a sequence that is complementary to a PRC2-associated region that encodes an RNA that forms a secondary structure comprising at least two single stranded loops; and/or e) a sequence that has greater than 60% G-C content.
 32. The single stranded oligonucleotide of claim 31, wherein the first chromosome is a chromosome of a first species, and wherein a sequence comprising the at least 8 consecutive nucleotides is located in a second chromosome between 50 kilobases upstream of a 5′-end of a homolog of the target gene and 50 kilobases downstream of a 3′-end of the homolog of the target gene, wherein the second chromosome is a chromosome of second species.
 33. The single stranded oligonucleotide of claim 32, wherein the first species is human and the second species is a mouse.
 34. The single stranded oligonucleotide of claim 31, wherein the oligonucleotide has at least two of features a), b), c), d) and e).
 35. The single stranded oligonucleotide of claim 31, wherein the oligonucleotide has at least three of features a), b), c), d) and e).
 36. The single stranded oligonucleotide of claim 31, wherein the oligonucleotide has at least four of features a), b), c), d) and e).
 37. The single stranded oligonucleotide of claim 31, wherein the oligonucleotide has each of features a), b), c), d) and e).
 38. The single stranded oligonucleotide of claim 31, wherein the oligonucleotide is up to 50 nucleotides in length.
 39. The single stranded oligonucleotide of claim 31, wherein the oligonucleotide is 8 to 30 nucleotides in length.
 40. (canceled)
 41. The single stranded oligonucleotide of claim 31, wherein the at least 8 consecutive nucleotides of the PRC2-associated region are in the strand of the chromosome comprising the sense strand of the target gene.
 42. The single stranded oligonucleotide of claim 31, wherein the at least 8 consecutive nucleotides of the PRC2-associated region are in the strand of the chromosome comprising the antisense strand of the target gene.
 43. The single stranded oligonucleotide of claim 31, wherein the PRC2-associated region is upstream of the 5′ end of the target gene.
 44. The single stranded oligonucleotide of claim 31, wherein the PRC2-associated region is downstream of the 3′ end of the target gene.
 45. The single stranded oligonucleotide of claim 31, wherein the PRC2-associated region is within an intron of the target gene.
 46. The single stranded oligonucleotide of claim 31, wherein the PRC2-associated region is within an exon of the target gene.
 47. The single stranded oligonucleotide of claim 31, wherein the PRC2-associated region traverses an intron-exon junction, a 5′-UTR-exon junction or a 3′-UTR-exon junction of the target gene. 48-52. (canceled)
 53. The single stranded oligonucleotide of claim 31, wherein at least one nucleotide of the oligonucleotide is a nucleotide analogue. 54-67. (canceled)
 68. The single stranded oligonucleotide of claim 31, further comprising phosphorothioate internucleotide linkages between at least two nucleotides. 69-93. (canceled)
 94. A composition comprising a single stranded oligonucleotide of claim 31 and a carrier. 95-103. (canceled)
 104. A method of increasing expression of a target gene in a cell, the method comprising delivering the single stranded oligonucleotide of claim 31 into the cell. 105-107. (canceled) 